Yes. Ponce de leon encountered the great paramount chiefdom, Calusa in florida, and writes of massive war canoes capable of housing dozens of archers. Calusa was a mississippian chiefdom that held political sway over a big chunk of central florida.
I'll be copying a post I've made on this before. Be sure to check out the original question for a few follow-up questions, but if you haven any follow-up questions of your own, I'll be happy to tackle them here.
Quigualtam's brown-water navy is a rather prominent example from the very early colonial era (1543), rather than the pre-Columbian era, but it does give a glimpse into the what was going on in the Mississippi valley at the time of contact. First, some background:
In the 1540s, Quigualtam was the dominant power in the lower Mississippi valley, part of a subset of the larger Mississippian traditions known archaeologically as the Plaquemine. As with so many historic Mississippian polities, the name Quigualtam is used for both the polity and its leader, so I'll be using it interchangeably for both here. We're not sure where Quigualtam's capital was. The Holly Bluff site is one option, though it appears to have been abandoned a generation or two earlier. If not there, then one of the neighboring sites in the Yazoo basin are the next most likely candidates.
The reason for the confusion is because, while de Soto and his expedition interacted with the Quigualtam polity and its outlying vassals, there's not confirmation that they actually managed to reach its capital.
The Spanish and Quigualtam officially made contact in 1542 (though in all likelihood, Quigualtam was well aware of the Spanish before this). At the time, de Soto was camped among the Guachoya, a lesser Mississippian polity on the west bank of the river that were vassals of Quigualtam. There, de Soto became too sick to travel. Through a Guachoya messenger, he had a messenger sent to Quigualtam. In this message, de Soto declared himself to be the son of the sun and demand that Quigualtam cross the Mississippi to pay his respects and offer tribute of whatever was most highly prized in his lands.
The messenger returned with Quigualtam's reply: he was unaccustomed to being summoned and, quite the contrary, everyone he knew was obligated to come to him, to serve and pay tribute. If de Soto came in peace, he would be welcomed by Quigualtam. If he meant to have war, Quigualtam would be waiting for him all the same. As the son of the sun, Quigualtam added sarcastically, de Soto should have no trouble drying up the Mississippi to ease his arrival. While this enraged de Soto, he was too sick to do anything about it. Before long, he'd be dead and his men were looking for a way back to Mexico.
No wishing to face Quigualtam, they attempted an overland crossing through Texas but soon had to turn back when they realized they could not sustain themselves foraging and pillaging in that region. Left with no other option, they built ships and took to the river in the summer of 1543.
On July 4th, they encountered Quigualtam's fleet. It consisted of some 100 war canoes. The largest canoes carried 70+ men - two columns of armed paddlers on either side, with a column of warriors in the middle. Some of the larger canoes also carried the fleet commanders, and could be distinguished by their colorful awnings. In fact, awnings or no, it seems like all the larger canoes were color-coded: the canoe, its oars, its crew, and their weapons were all either painted in or wearing the same color. The whole fleet moved in well-practiced formations, singing to set the pace for the oars.
When the attack came, some of the crew of the larger canoes jumped overboard. Of these, a few positioned themselves to steady the canoe to serve as a more stable platform from which those still on board could fire their bows. The rest swam to the Spanish boats, staying underwater most of the way to hide their approach, and boarded. The initial clash consisted of a small portion of the Spanish fleet attempting to disperse Quigualtam's fleet, and failing miserably, while the rest of the Spanish fled. Four of the would-be conquistadors managed to escape back to the main body of the Spanish fleet - the other 20 or so men were either killed, captured or missing. Regardless, they were never heard from again.
Quigualtam's fleet pursued the fleeing Spanish for the rest of the day. After the initial assault, they kept their distance. Circling the Spanish, they fired arrows on each boat in turn but never came closer than bow-range, though they could have easily overpowered them had they tried. Perhaps they were concerned that Spanish were holding their more fearsome weapons in reserve and were keeping a safe distance. Alternatively, perhaps they were less interested in wiping out the Spanish than they were in sending a message that Quigualtam was not to be messed with.
As night fell, it seemed that the Spanish had finally escaped Quigualtam's pursuit. But in the middle of the night, the war chants and songs began again. The chase kept up until noon the next day, when Quigualtam's fleet turned back. The Spanish finally had a moment to breathe a sigh of relief. But just a moment. Soon a second fleet of another fifty war canoes picked up where the main fleet left off. This fleet made several close-quarters attacks and managed to rescue or claim as their own (we don't know their motives) some of the native captives held by the Spanish.
When the Spanish finally escaped this second fleet the next day, a third (though substantially smaller, only consisting of seven war canoes) awaited them. While the canoe fleets became smaller and more infrequent, this pattern essentially kept up until the Spanish reached the mouth of the Mississippi around July 16th. As they approached the mouth of the river, the man among the last fleet delivered this final warning (translated for the Spanish by one of the Native captives they still had with them):
"Thieves, vagabonds, and loiterers who without honor or shame travel along this coast disquieting its inhabitants, depart from this place immediately by one of the two mouths of the river, if you do not want me to destroy you all and burn your ships. And see to it that I do not find you here tonight, for if I do, no man of you will escape with his life. If we possessed such large canoes as yours, we would follow you to your own land and conquer it, for we too are men like yourselves."
The Haida Indians of the Queen Charlotte Islands in the Pacific NorthWest made raids on other PNW Indians on the waterways.
They tied cedar bark ropes to heavy stone rings that were hurled to smash enemy canoes and that could quickly be retrieved for subsequent throws. A stone weighing 18 to 23 kg (40 to 50 pounds) could shatter the side of a dugout canoe and cause it to founder. Most tribes avoided sea battles with the Haida and tried to lure them ashore for a more equitable fight.
http://www.historymuseum.ca/cmc/exhibitions/aborig/haida/havwa01e.shtml
The vessels used by the natives of the PNW were dugout canoes, carved from a single, huge log and steamed open so it could be wider than the log it was made from; here's an example 17 meters by 2 meters:
http://www.historymuseum.ca/cmc/exhibitions/aborig/haida/havct01e.shtml