Cities are big places, but not that big. They still sometimes have to go out of their way to justify why the Avengers and the Fantastic Four can't respond and why Spider-Man is the ONLY hero around to stop Dr. Octopus or whatever. it can be a bit difficult to believe that they are always busy at around the same time another hero has a crisis that requires a solo adventure, but fans just roll with it.
Marvel's New York is full of so much fictional stuff and events now that it might as well be a fictional city. Again, what difference does it make? There are issues with geography, but I don't think many of DC's fans care about where these fictional cities are located. It's changed so much over the years it doesn't even matter.