With no offense meant, I think the whole notion of it being based on New York has been vastly overblown (not in this thread - just generally). Yes - I know Masuda said it was inspired by it, but I think what he meant when he said that and what people have taken it to mean are obviously different things. I mean - just look at it.
The overhead view of Castelia City bears some resemblance to lower Manhattan, and that's really about it. By the time you get out to where Long Island would be and find that it's a Mexican shanty town straight out of a Sergio Leone movie with a volcano looming overhead (or when you come out on the other side of that volcanic mountain and find yourself at a Caribbean resort, or when you go south from Castelia and find yourself in a windswept desert surrounded by steep canyons), I think you should be getting past the idea that it's really, in any broad sense, anything other than VERY loosely based on a fairly broad range of environments, most of which have counterparts in or near North America. And that's about it.