Native Americans did in fact have permanent cities, like notably Cahokia in what's now Illinois. There were also some earlier colonial settlements along major waterways like the Mississippi. It's likely there were quite a few permanent cities that were lost to time because they weren't built with materials that would last centuries of abandonment. Notably there are thousands of effigy mounds dotted across the landscape of basically the entire Midwest, which is a very permanent sign of long term habitation or at least locations returned to frequently enough to be worth creating such a monument