Well, it's still not that great. The federal government did not treat them well, but a white population that didn't even have those nominal rules holding them back probably made things worse before they got better. Ironically, however, the isolation of these reservations (and their lack of urbanization) meant Native Americans were probably not hit as hard as other minorities in the U.S.
In the eastern half of the continent, it's likely Native American ethnicities and cultures have been pretty much absorbed, except for perhaps a few pockets in New York, Florida, Michigan, and especially Wisconsin. The overlay of a map of American reservations and the populations shows northern Wisconsin and Minnesota are isolated from most of the frontier communities. The populations aren't going to be sizable, but most of them are the size of regular villages in the present day anyways.
It's possible the most concentrated area of Native American society is Northwestern Arizona. Today is the location of the Navajo nation, and it may be isolated and yet robust enough to have a thriving native culture in the world of Medieval America. Around 100,000 people live around this area--a third of the population today, a little less than a third in that region today, which is pretty good for the continent and the region in particular. If one were to take the five million or so who identify as natives, that's one and a half million. A third of that would be 500,000, which I think would be the minimum for distinctly and definitively indigenous people. However, their contribution and influence, from both a biological and social influence, would be much, much wider.
