In broad and liberal generalizations:
County/Knife&Gun club: I like Downstate and Jacobi equally and would pick one or the other over Lincoln.
Overall great eperience: Bellevue & SLR in Manhattan, Methodist in Brooklyn. I personally also think NYH Queens would be great, if you can make the commute; they are a VERY young program, but they see very diverse patients and pathology.
There are many other excellent programs in NYC and metropolitan area, those are just what came to mind on the spot.
If you are _truly_ set on going to NYC, and depending if your home institution already have an EM rotation, or if you have the time in your schedule, you might consider doing two rotations in NYC. For example, if you rotated through Downstate or Jacobi or Bellevue, then rotated through SLR (or reverse order), you would have gained a lot of valuable perspectives: 3 versus 4, county versus not, academic or not, etc. Plus, you certainly would have committed yourself--in the minds of the PDs--that you want to be in NYC. This will be helpful and should pay dividends. Of course, if you don't have the time or simply don't want to do two away rotations, that's certainly fine and don't sweat it. Doing one away at your region of choice is enough.
Regardless, this confirms what you already know--doing an away in the region you want to be in is very helpful.
Best of luck!