Not everybody who works for Marvel has necessarily been to New York. Carlos Pacheco, Salvador Larroca, Grant Morrison, and lots of other creators live outside of New York and even the US and turn their work in via the Internet or the mail or whatever. It's not like they have to actually go into the Marvel building, write or draw their pages, and then go back home every day. A lot of work is done through correspondence. I don't think that's the reason Marvel uses New York.
Also, DC's comics have creator changes as much as Marvel's, and their fictional cities stay pretty consistent despite the fact that it's impossible for any creators to live in them in reality. Keystone, Metropolis, Coast City, Central City, Smallville, and most of the other fictional cities in the DC universe have recurring landmarks throughout their appearances.
Basically, I think the reason Marvel's heroes are mostly based in New York is because back in the '60s, when most of the writers and artists did actually work out of the Marvel offices, Stan Lee liked writing about New York and the early artists liked to draw by looking out their windows for references. It was convenient to set everything in New York back then because everyone was there anyway. Things have changed since then, though.