I’m away from my books for the weekend, so here are some older questions that I’ve answered that you’ll find interesting. Also, be sure to check out our Mega-AMA on the Pre-Columbian Americas and the relevant section of our FAQs

• Did Native Americans have accurate maps of North America? What groups had the most geographical knowledge of the continent?
• Is there any reason why the Native American civilization never was able to work metal?
• How sophisticated was the Iroquois Confederation's government at its peak?
• Did Native Americans smoke marijuana?
• Did Native Americans make roads?
• How much contact did the Mesoamerican cultures like the Mayans/Aztecs have with Indian groups in what is now the United States and Canada?
• In a talk I saw recently, David Graeber implies that (at least one) Native American Culture found by Europeans could be the byproduct of a revolutionary ideology that brought down earlier civilizations in the area. Is there any evidence to support this?
• Why are there no ancient Native American cities in North America?
• Did Native Americans really use "all parts of the buffalo"?
• What was happening in North America during the life of Jesus?
• Monacht-ape’s Journey
• Why is there nothing old present around Americans?
• Miami Kinship
• Is there any evidence of ancient structures (Like those in Mesoamerica) existing anywhere in the United States?
• Could Native Americans be considered communists?
• Why are there no pyramids or temples in North America, but there are so many in South America?
• Do we have any examples of pre-columbian Native American humor?
• The Lost “Kingdom” of Saguenay
• How accurate is the popular US perception that Native Americans lost their land "because they didn't understand the concept of ownership?"
• There was supposedly a reasonably complex Mississippi Valley civilization before Europeans arrived. What would the biggest settlement in the area, and what would it have looked like?
• Is there any sort of historical accounts, written or passed down orally, of major events or battles in North America before conquistadors and others arrived?
• Suppose you were sent back in time to New Jersey (or where New Jersey is now) in AD50 and then AD1050. Could you easily tell which was which by observing the native Americans?
• To what extent were Precolumbian Native American Navies used militarily?
• Were any canine breeds indigenous to North America, and have any of those breeds withstood time to become a common breed among our domestic pets today?
• Siege warfare in pre-Colombus Americas - How prevalent was it? What were the tactics and technology used?
• It's gonna be negative -30 (factoring windchill) in Boston the next couple of days...how did our ancestors survive this?
• Jigonsaseh: The Mother of Nations
• What differences caused the Mesoamerican societies to be much more successful than Eastern North American societies?
• Were there any seafaring cultures centered around the Great Lakes region of North America?
• How did Native American Indians adapt uniquely to their environment?
• What methods did the pre-Columbian American Indians use to gather precious metals and stones, and were there any surprising materials they prized the way Europeans prized precious metals and gems?
• How did Native Americans deal with the harsh New England winters?
• When the first colonists came to North and Central America, how come the Native Americans never fought back when they first arrived?
• During their 'Mourning Wars', the Haudenosaunee would capture and assimilate their enemies. What was the process of assimilation like for individuals captured, or for entire tribes, for that matter?
• What native tribes lived in Spanish-claimed Florida, before the Seminole arrived? How were the politics and trade between these tribes?
• How much do we know about how the Iroquois would have hunted?
• How can I learn about the indigenous inhabitants in my area (Ohio)
• Were there any civilizations near the Ohio River and if so who were they?
• Were native american tribes aware of the mound builder civilization?
• did the native Americans John Rolfe's group met in Virginia follow a religion that was at all related to the religion of those the pilgrims met in and around Plymouth?

I'd recommend starting with 1491 by Charles Mann. It's an informative and fast read, and gives you a good idea of the scope and timeline of the rise and fall of key civilizations in the Americas.

When looking through some of the many other excellent answers /u/Reedstilt posted, keep in mind that the Spanish were entering the U.S. Southwest and Southeast about the same time as the English were entering the Northeast/East. The colonial history of North America is just as much a story of Spanish and French (and even Russian) colonialism as it is of English colonialism.