We have several lines of evidence that allow us some insight into large-scale Native American conflict before contact. Ethnohistory and oral tradition, as well as archaeological and bioarchaeological information together can help us understand some aspects of the role of warfare in Native North American populations.

For example, historians and archaeologists compiled Haudenosaunee oral tradition with Owasco archaeological evidence in the form of village defense style and weapons, to determine that small scale raiding was likely the most common form of warfare in the Eastern Great Lakes before the formation of the Iroquois League.

Typically, 10-100 men would cautiously approach an enemy village, either attacking it directly or, more commonly, ambushing its residents as they left on their daily business. The raiders typically killed as many men as they could, took scalps and captive women, and fled homeward until they were sure they were not being chased. –Snow (1996)

Typically these raids were conducted against non-Iroquoian nations (external warfare), but there is evidence of warfare between distinct Oswaco groups as well (internal warfare). Haudenosaunee oral tradition supports this perspective, saying Deganawida/The Great Peacemaker grew tired of the endemic raiding and bloodshed. He had a vision of a united Haudenosaunee League and called together the leaders of the Onondaga, Oneida, Mohawk, Cayuga, and Seneca in hopes of uniting the nations together.

More often we lack the direct oral tradition link to the history of a site, and we are limited to archaeological and bioarchaeological analysis. The best evidence for large-scale conflict is the case at Crow Creek. The Crow Creek Massacre is one of the largest pre-Columbian skeletal assemblages attributed to a violent encounter in North America. Sometime around 900 CE the ancestors of the Mandans built several earthen structures in the south central portion of modern-day South Dakota. Eventually the Caddoan-speaking ancestors of the Arikaras replaced the Mandans (no indication the replacement was by force) and increased the settlement to a decent-sized community of roughly fifty-five earthen lodges.

For unknown reasons, in roughly 1325 CE, at least 486 individuals at Crow Creek were violently killed. Evidence of the massacre was discovered in 1978 when skeletal remains eroded out of a fortification ditch. Analysis of the remains indicated extreme violence during the attack, and parts of the victims appear to have been taken as trophies by the attackers. The village appears to have been sacked and burned. Based on analysis of the skeletal remains we suspects many of the victims were malnourished, suggesting the conflict might have occurred due to scarcity of resources (Calloway, 2003).

The state of the remains indicates they were exposed for a period of time and subject to the typical animal scavenging expected on the Northern Plains. Sometime later the remains were gathered together, placed in a communal burial, and covered with a thin layer of clay from the nearby river. We don't know if survivors of the attack, their kin, or someone altogether different were responsible for cleaning up the battlefield.

The archaeology of warfare in North America is not my primary focus, I tend to read more of the bioarchaeology literature, but check the sources below if you are interested in learning more.

Sources

Andrushko et al., (2005) Bioarchaeological Evidence for Trophy-Taking in Prehistoric Central California

Calloway (2003) One Vast Winter Count

Lambert (2002) The Archaeology of War: A North American Perspective. Journal of Archaeological Research.

Milner (1999) Warfare in Prehistoric and Early Historic Eastern North America. Journal of Archaeological Research

Smith (2003) Beyond Palisades: The Nature and Frequency of Late Prehistoric Deliberate Violent Trauma in the Chickamauga Reservoir of East Tennessee. American Journal of Physical Anthropology.

Snow (1996) The Iroquois

Willey and Emerson (1993) The Osteology and Archaeology of the Crow Creek Massacre. Plains Anthropologist

For clarification: are you asking about what battle strategies/tactics were like, or are you asking if we know pre-Colombian American war history (what battles were fought between whom, when, etc.)?

I tried to post this as a reply to another user, but his comment was deleted, so here goes.

The Aztecs (er...Mexica is the more correct term) and Inca were powerful, sophisticated empires with detailed recorded histories at the time of conquest. For example, there are pretty good records of the rise of the Inca empire in the 1400s. The Mexica erased many of their old records at one point and re-wrote their histories, but we still have records of most of what happened from that point until 1519. In fact, there are more writings in the ancient Nahuatl language than in Ancient Greek! (source 1491 by Charles Mann...as is most of this) The tribes of North America didn't have the sophisticated writing and recording systems (that's not to say that they weren't sophisticated societies however.) We do know a few details, such as the story of how the Haudenosaunee (Iroquois) confederation came together under the Great Law of Peace. Also, there would not have been large scale battles since most of the tribal groups were relatively small. We do know that some tribes warred in Pre-European America. For example, Tisquantum (Squanto of Pilgrim fame) found his village destroyed by the Wampanoag prior to meeting the Pilgrims, but not before encountering Europeans.

Also known as the Iroquois Confederacy, the Haudenosaunee developed as a method of ensuring peace between the Five Nations (Seneca, Cayuga, Onondaga, Oneida, and Mohawk) which had until that point been caught in a cycle of retaliatory warfare. This period of Iroquoian warfare and its ultimate resolution is perhaps the most famous episode in the oral history of Pre-Columbian America, but it’s not the only instance of warfare in the Iroquoian oral record.

Another talks abouts about a long period of warfare between the Alligewi (sometimes Talligewi) on one side and the Iroquois (prior to the formation of the Haudenosaunee) and the Lenape on the other. The exact identity of the Alligewi is currently unknown, but at the time they inhabited the Ohio Valley. After generations of war, the Iroquois-Lenape alliance drove the Alligewi south (a prominent idea of who the Alligewi might be identifies them as the ancestors of the Cherokee who are known to have migrated south along a similar route). The victory over the Alligewi is attributed to the Iroquois’ use of bows, which the Alligewi didn’t have or weren’t as skilled with. With that in mind, this narrative’s archaeological counterpart may be the Late Woodland period in Ohio Valley archaeology, beginning around 500 CE, when new populations armed with bows began moving into the area from the north and east.

Another notable incident of warfare in the oral tradition occurs during the time of the ninth Adoraroh (the Adoraroh is the chairman of the Haudenosaunee Grand (Men’s) Council, a position he occupies for life). At the time the Haudenosaunee were at war with the Mississauga (currently an autonomous branch of the Ojibwe, but whether that applied at the time is unclear - the written form of this account, from 1825, might be a bit anachronistic with its terminology). The Jigonsaseh, the equivalent of the Adoraroh on the Women’s Council, attempted to negotiate peace between the Haudenosaunee and the Mississauga and hosted a Mississauga delegation in her home for that purpose. During the negotiations, the leader of the Mississauga delegation was killed by two Seneca men. To maintain the current cease-fire in the war, Jigonsaseh turned the two men over Mississauga for punishment and immediate traveled to Onondaga to consult with the Grand Council there. While the tradition does not specify what occurred during this meeting, it does allude that a political rival reached the Grand Council first and poisoned them against Jigonsaseh. Regardless, she returned home soon after and called upon her local war chief to begin reaching out to non-Haudenosaunee allies. Jigonsaseh, the western population of Seneca to which she belonged, and her allies fought against the the rest of the Haudenosaunee. A recent interpretation of this episode describes it as a civil war over whether the Jigonsaseh, in her role as principal peace-keeper, is permitted to extradite citizens of the Haudenosaunee in order to maintain peace. In the 1825 version I’ve been focusing on here, this civil war ends in draw and a return to the status quo. In other version, written down in 1881, this incident is wrapped up with others that the 1825 includes as separate events and ultimate leds to the expulsion of the western Seneca from the rest of the Haudenosaunee who form their own confederacy (the Erie). The 1881 version also uses this incident to explain why the position of Jigonsaseh was abolished for many years.

As far as what these wars might have looked like, before the introduction of firearms, Iroquoian warriors went into battle wearign rod- and slat-armor. That particular image is based on a Wendat (Huron) warrior, but similar armor has been described for the Haudenosaunee as well. Common weapons included bows, thursting spears, and the ball-headed club. A large army could number into the low thousands. I’ll give some early historic examples since the oral traditions generally don’t keep track of this sort of thing. During the war against the Erie in the 1650s, all five of the Haudenosaunee nations contributed forces. The Mohawk were the least involved and contributed 700 warriors; the Onondaga contributed 1200; we don’t know the numbers for the other three, though the Seneca likely contributed as much as the Onondaga at the very least. On the other side, the Erie were fielding at least 2000 warriors.

Villages, particularly those on the periphery, were defended by strong palisade walls which later European forces often found challenging to confront. The Iroquoian methods of siege warfare involved firing flaming arrows over the walls. When a village could be approached from the water, Iroquoian canoes allowed for swift attacks, then could be drawn from the water to provide cover as the warriors approached, and finally, propped against the palisade as a siege ladder. Once the warriors had closed the distance to the wall, they could use the same loopholes the defenders employed to fire into the village or set fires on the outside to lure the defenders out. However, the palisades usually included walkways along the top, from which the defenders could fire down on the attackers or rain stones down on them.

Sometimes, especially before Europeans arrived, formal battles would occur well outside of a village, with opposing forces lining up against each other before charging into combat.

Ideally, captives were taken alive - which greatly heightened the prestige of the warrior who performed the capture. Once the warriors returned home, all the captives were divided out among the participating nations then to participating families within those nations, though typically on the most prominent families received a share of captives. Women and children were usually adopted into the new families. Men often were as well, but not always. Rather infamously, captive men might be executed by torture. While the capturing warriors might be able to make recommendations regarding a captive’s fate, the ultimate decision rested in the hands of the women receiving the captive. If they had recently lost a family member, the captive would more often be executed to avenge the prior death; if the family’s grief had passed, the captive would more often be adopted and assume the role, to varying degrees, of the deceased.

As a final note, unrelated to the Haudensaunee, you might be interested in this post concerning the river fleet of Quigualtam, along the Mississippi.

I'm a bit late to the party here, but let me talk about warfare and combat in Alaska. All Alaska Native groups experienced some level of local or regional conflict. The quantity and degree of these conflicts varied from place to place. As Ernest Burch Jr. wrote in 1991:

"... the precontact population of Alaska was divided into a large number of nations, or countries. These nations were tiny ones in terms of population, but they were nonetheless just as distinct from one another as Israel and Syria, or as Germany and Austria, are today. ...

The tiny nations of Native Alaska had their great leaders and their villains, and their triumphs and tragedies, just as the great nations of Europe and Asia had theirs. The citizens of these tiny nations could and did engage in international intrigue and in war. They engaged in international diplomacy; they created international alliances and regional power blocks; and they participated in international trade."

Burch in 1974 wrote one of the classic papers on Alaska Native warfare, "Eskimo Warfare in Northwest Alaska," and his work has been carried a bit by subsequent scholars. In general ─ and that's a term that's tough to use with a territory as large as Alaska ─ combat was a matter of surprise attacks by raiding parties carried long distances by small boats. Many groups had fortresses or refuge areas ─ referred to as "refuge rocks," these could be as simple as an easily defended point of land ─ to take refuge from these raids.

Laminar armor was used almost universally in Alaska, with vertical slats of wood across the chest and back. Helmets of varying construction were employed, as were shields. Spears, bows, clubs, knives, axes and other hand weapons provided offense. Coastal whalers are known to have poisoned their weapons, and it is possible these poisons were used in warfare as well.

In southwestern Alaska, the Unangan people of the Aleutians (commonly called the Aleut), fought with the Alutiiq/Sugpiaq of the Kodiak archipelago, the Chugach of Prince William Sound and the people of the Alaska Peninsula. As Steve Langdon writes in The Native People of Alaska, "Hostilities often took the form of raids in which small groups of men, usually less than 10, attacked another village to avenge some insult or theft or to obtain women as slaves. Men who participated did so generally by choice rather than by order."

There's a story called "How the Men of Qilangalik avenged their wives," told by Makari Chimovitski in 1933 in Tales of the Chugach, that illustrates this practice. One summer, the men of Qilangalik, a Chugach village, went seal hunting and left their wives at the refuge rock at Johnstone Point on Hinchinbrook Island.

At the same time, an Alutiiq war party arrived and found the women at the rock. The women attempted to fool the Kodiak warriors into thinking the men were still there by making mustaches of bear fur and brandishing spears, but the ruse was exposed when one woman's mustache fell off. Some women resisted and were killed; others were taken as slaves or wives.

That winter, the Qilangalik men retaliated by traveling to Kodiak. During a snowstorm, they attacked and recovered their wives as the Alutiiq raiders were eating dinner. Some of the men didn't want their wives back and instead took Alutiiq girls back to Chugach territory.

Along the Bering Strait, the Yu'pik of St. Lawrence Island and the Inupiat of Seward Peninsula found themselves frequently in contact and conflict with the Chukchi of what is now far eastern Russia. Raids and counter-raids are described in Dorothy Jean Ray's The Eskimos of Bering Strait.

Coastal trade was a significant thing in the pre-Contact era, with long-distance journeys conveying copper, whale products, dentalium shells and furs. Violating a trade deal or insulting another group could bring reprisals. The Chugach of Prince William Sound frequently fought with the Eyak (in the vicinity of modern Cordova), because the latter had an influential position as the intermediary between the Chugach and Tlingit trade of Southeast Alaska.

The Tlingit, meanwhile, were one of the best-organized Native groups in Alaska, but they too were under stress in the years immediately before Contact. Two hundred or so years before, what is now southern Southeast Alaska was invaded by the Kaigani Haida from what is now British Columbia.

So out of curiosity was there any large scale native american battles where both sides fielded large armies(say, in the thousands)?

Almost along the same lines but how often was lacrosse used as an alternative to war?

paging /u/Wades-in-the-Water -- I think you could give a pretty good answer here, if you still reddit.