Brooklyn is the only part of NYC where I can imagine having a dog of any kind. I won't pretend to be even vaguely acquainted with anything but Brooklyn and Manhattan, though, so if an actual inhabitant of NYC says otherwise, trust them over me. Commuting from NJ, as Gretchen suggested, might be more doable; that might be a good option to look into.
Country-to-city can be a difficult transition for a dog who's accustomed to the quiet rural life, and NYC is a LOT denser, noisier, and more congested than even the most crowded parts of Philly. More expensive, too, for everything from dog food to vet care -- and it can be very hard to find places that'll rent to a tenant with a big dog of an "aggressive" breed.
You can make it work, if you're willing to put in the time and effort (and money), but it does take some doing. If I were in your shoes, I'd spend some time thinking honestly about what would be in the best interests of my dog.
ARCHMX TDCH Pongu the Insane, CD-C, RE, RL1X6, RL2X5, RL3X2 (GSD mix, b. Apr 2010)
Crookytail the Tigerwuff, RL1, ITD (Akita mix, b. Jan 2011)