I grew up in the midwest, where many of the nearby cities have indigenous names (Milwaukee, Chicago, Minneapolis, most small towns in Wisconsin). But now i live in California, where all the major cities i know of have Spanish names (San Francisco, Palo Alto, Los Angeles, San Diego). I imagine this is due to differences in Spanish vs French/English colonial policy, why did the Spanish not keep any indigenous city names while the English did?
I'm not sure your premise is fully accurate. There are tons of cities in the Midwest with European/American names, such as Cleveland, Columbus, Cincinnati, Indianapolis, Grand Rapids, St. Louis, Madison, and Green Bay.
Tuscon is an example of a city that the Spanish gave an indigenous name.
To me Western New York is an area that stands out for distinctively indigenous names.