Navajo alone has 170,000 speakers. The problem with having a native american majority city isn't that the numbers aren't there, but that for legal and cultural reasons, the right to call oneself a "native american" is heavily restricted. It's kind of like the opposite of African-American: if you're 1/8th black or more, you get called African-American. But to be legally and culturally "Native American", you have to be enrolled with a tribe, and raised in with a Native American background. That's because, since the US government has finally gotten around to honoring the treaties made with native american tribes to at least some degree, native americans get a number of privileges. So, naturally, the federal government wants to restrict the amount of people who can claim these privileges as much as possible.
So yes, it would have been easily possible from a logistical perspective for Native Americans to form a large city, but the fact that Native Americans tribes can't really assimilate new members (a few historical oddities like the Black Cherokee excepted) means that these cities eventually just become ordinary cities with a Native American heritage.