Only New York though? Maybe it's different for Americans, but I wouldn't recognize any other American city. I can't believe that the difference is simply that most Marvel heroes operate in a single city though.
You seem to be missing the point - the point is not, specifically, NYC. The point is
REAL PLACES. That includes NYC. But it also includes Chicago, LA, Washington DC. It is New Orleans, Jersey City, and so on...
When a story is placed in Metropolis, you can't really assume much - we only know what the author specifically tells us about Metropolis, and that typically isn't much. In doing so, the author is positioning their story such that the location doesn't really matter. Metropolis becomes code for "abstract clean large city" and Gotham is code for "abstract gritty large city", but the particulars beyond that are not relevant.
We know a lot more about NYC, and the author can use that understanding to great effect, if they know what they are doing. To see an extreme example of this, see
Amazing Spider-Man #36, from 1999. Fans may recognize the cover:
The characters lived there, and so their emotions about their home became relevant, and connected to ours. To have this happen in Metropolis includes a layer of abstraction that gets in the way of relating to the story.
There's a genre point here - the original technical difference between "high fantasy" and "low fantasy" was not how much magic was in the world, or how epic the storyline. It was location. Low fantasy took place in our world, high fantasy took place on some other world.