Hiya -
Can't give you too much help, but since no one else has chimed in...
I took Organic 1 as a summer class at Brooklyn College. Liked the prof, the class was tough (30 started, 14 sat for the final) in a manner that i thought was appropriate. The labs were well run. While it is not as nice as a private college will tend to be, for a CUNY school it was pretty impressive (much cleaner, better run than Hunter, where I did most of my post-bac classes).
The MD program links to SUNY Brooklyn, right? Also a school which is good, but suffers from the 'not as nice as a private school' problem, but where I will probably be going next year. If the program locks you out of applying anywhere else, don't do it - if you are coming out of Stuy, I bet you'll do well enough at any college to get in to SUNY on your own, and you don't want to limit your options too early in the game. But if it gives you a direct feed into SUNY while leaving you free to look at other stuff, it sound pretty win-win.
Hope that helps.