Central Mexico filled with cities which were extant settlements prior to the arrival of the Spanish, many of them long prior to then. First off, Mexico City today encompasses a large portion of what was formerly the basin of Lake Texcoco, spanning across many formerly independent cities. Texcoco, Tlacopan, Atzcapotzalco, Culhuacan, Chalco, and innumerable other cities are part of the metropolitan area of Mexico City.

Even outside of that city, it's hard to throw a rock without hitting a town or city in Central Mexico that does not have pre-Columbian roots. There are notable examples like Colima, Cholula, and Tlaxcala, but there are ubiquitous smaller towns, often marked out by their indigenous names. Cue the obligatory AskHistorians Podcast shout-out, wherein I note the last couple episodes (13 & 14) talked a great deal about urban areas in present day Michocan which are very much still there.

The real problem though is how the phrasing of your question sets boundaries on the discourse over pre-Columbian settlements still extant. It begs the question over what is a "city" as opposed to a "settledment," which is a question that any number of academics might start a fist fight over. There's the bigger question as to why this even matters (it feels a bit like the long train of "justify the existence of Native American cultures in a test that other cultures do no have to take"), but let's put that larger question aside and assume you're just here for the love of knowledge.

First off, we have the question of many previously inhabited settlements which are currently located within the outskirts of extant urban areas. Teotihuacan is the obvious one that we'll skip given the parameters of your question, but there is also Cahokia and Chan Chan. The former is basically in the suburbs of East St. Louis and the latter is not that far of a walk from Tujillo. The indigenous urban core areas are no longer actively inhabited -- they are preserved as historical sites -- but does a new settlement right next door then disqualify the site from consideration? It's not like Italians are still doing much business in the old Roman Forum.

Then there's the question of present day major metropolitan areas founded on small settlements. Boston was previously home to Indigenous dwellings prior to European settlement. Atlanta was previously a small Creek village before taken over by Euro-American settlers. Same with Dahlonega, GA (site of the US's first Gold Rush), to give a smaller example, although the group displaced there was Cherokee. Oaxaca City was formerly a minor Aztec outpost before being turned into the governmental center of the state of the same name.

The list of modern day cities and towns founded on prior Indigenous settlements is almost literally innumerable. The same reasons the prior groups established permanent residences in a particular area in the past are in large part what drew later groups to the area. This applies equally to later Indigenous groups overtaking an area as well as the later European arrivals. There's also the question of how to count places like Plymouth, MA, which was founded in an area left deserted following an epidemic among the previous Indigenous inhabitants.

The answer to your question though is "Yes, a great deal." The exact number though, depends on how you define your terms.