Also, which program did you get accepted to at City College? There's a 5-year MD program there where you complete your pre-medical coursework and pre-clinical classes the first three years, and then move onto finishing your clinical rotations with either SUNY-Downstate, Darthmouth, Albany, or NYU. Obviously, if you got accepted to the Sophie Davis program... go there and save yourself the hassle.
As a SUNY alum, I'd say go to SB. Just be aware that a lot of students leave on the weekends and it can be a bit of a ghost town, so I've heard. Between City College or Hunter... I had a friend who studied bio at City College doing evolutionary studies and she really enjoyed it and has gotten amazing opportunities out of it (internship in Madagascar!!). But this is very dependent on what you want to study. "Pre-med" is just the required courses, but you can be whatever major you want. SB, as a university, will provide more diverse majors and course selection. If you're in the honors program at City College, I feel that's a much stronger science program than Hunter IMHO, but both schools are probably the two CUNY's one would want to go to. Hunter has a lot of commuters as well. City College will provide more of an NYU lifestyle, while SB will give you more of that collegiate experience. I could have went to NYU but I chose a SUNY due to how amazingly cheaper it is for the same education and opportunities, and because I wanted to experience university life on my own and something other than NYC after growing up there my whole life. Just a few things to keep in mind
Good luck with your future studies and which school you choose. It ultimately comes down to where you be happiest, as that's where you'll succeed best.