They are both great schools and you can't go wrong with either.
Make your decision based on where you want to spend four years, and where you want to be after. At either school, you can do your elective rotations anywhere, but if you think the NY area is where you want to end up after school, I'd pick NYCOM (and if you think the Philly area, go with PCOM). Reason being is you'll get more face time and experience in those hospitals which will help when it comes to applying to residencies.
By the way, NYCOM isn't really in New York City, it's on Long Island. I don't know exactly how far away it is from the city (maybe an hour or so, someone correct me if I'm wrong) but it's more in the suburbs than the Big Apple.