...then I'll keep going with the NYC side.
Isshu isn't based off of New York City. It's based off of the shape of the 3 landmasses that comprise the focus of NYC's metropolitan area. Hiun City and nearby Liberty Island are direct references to the NYC and it's statue of liberty, and sure, Hiun City is most likely based off of the harbor area at the front of Manhattan Island, but the rest of the region is just as imaginative in its sources, restoring most of the rest of the area to its natural state, even adding steep mountains at the sides for interest.
For those who want to go about debating the accuracy of Isshu and how the mountains don't fit in, Kyoto, Japan, which Ecruteak City is based on, is far closer to Lake Biwa, which is what the Lake of Rage is based on, than the games suggest. I'd like to think they'd be able to have a creative license with this sorta stuff. After all, it's a shape they really borrowed. I don't think it's just American influences they've borrowed for the region, but modern, western culture which has been more of an influence in these new games.