There are obvious plusses and minuses to each location (e.g. hot sticky Charleston summers, bitterly cold Upstate winters, fun but uppity Saratoga Springs, fun but redneck Charleston...) but judging from my own experience at Ballston Spa compared to what my classmates told me about the MTSs, the New York prototypes are more laid back than their Charleston counterparts. Of course, it all depends on your particular chain of command...
Me, I'm glad I got to experience both places (I liked both Charleston and Ballston Spa for different reasons), and despite an extended shutdown we didn't have too much trouble qualifying at MARF. Either way, I'd advise living downtown (either downtown Saratoga or Charleston) for the best off-duty time.