I think (and it depends on personal preference, and where in NYC u wanna be, and what u are looking for, etc.) the most "prestigious" programs are....
Number one would be Columbia ( I think almost all would say this is the number 1 place). Cornell, Mt. Sinai and Einstein are all sorta similar, depending on what you are interested in. Einstein has a proper children's hospital. I"ve heard mixed reviews about NYU, and LIJ is kinda in NYC, and is solid, though I am not sure if those guys are overworked or not...I've heard they might be. After that, Jacobi is pretty good, not as sure about the rest.