Some pearls of wisdom that you might find helpful, based on my classmates' and my own experiences:
1. Try to get North Shore Manhasset for your Medicine clerkship. However, the unspoken rule when I was a student was that only the top students in the class would actually be allowed to rotate there for the Medicine clerkship, despite Matchstix. I'm not sure if this has changed.
2. I found that one of the most underrated hospitals for Medicine in the NYCOMEC system is Maimonides Medical Center in Borough Park. The general medicine rotations were outstanding and many of their subspecialty medical faculty are actually very well known in the world of ACGME academia. Doing well there and scoring a letter from one of these attendings could go a long way if you're interested in an ACGME residency.
3. St. Barnabas, on the other hand is one of the most overrated hospitals in the NYCOMEC system in my opinion, and the only reasons students go there are the osteopathic General Surgery, EM, and Radiology residencies. If you're gung ho about doing an AOA residency in one of these fields, it might be the right choice. If you aren't, there are better hospitals in the system in terms of teaching and clinical exposure.
4. Some of the hospitals are great in a particular area but lousy for others, and it's important to glean from your upperclassmen which those are. Getting back to Maimonides, I recall many people who did Ob/Gyn there were very dissatisfied, because unless you were a female and Jewish you weren't allowed in the delivery rooms or to perform exams. Unfortunately, the non-Jewish patients tended to be Muslim, who also objected to having males in the rooms.
5. If you want to see a lot and do a lot on your Surgery and Ob/Gyn rotations, you go to the big inner city hospitals or to NUMC.
6. Don't seek to do a 3rd year clerkship someplace cush because you feel it won't be relevant to whatever field you think you're going into. I did surgery and Ob/Gyn in the inner-city hospitals in Brooklyn, and feel like I learned a lot by being a lot more hands-on than students who just cut out of their cush rotations daily and just read for the shelf exam.
7. If you take your education seriously, avoid the tiny community hospitals that NYCOMEC has affiliated with where you're basically doing a preceptorship rather than a proper clerkship. This pretty much excludes 90% of the Long Island affiliations. A good rule of thumb is that if the hospital is big enough to support an ACGME residency in the particular discipline (not an AOA residency, as the accreditation standards are laughably inferior by comparison), it likely has a decent educational structure in place so you won't be wasting your time. Also, if students from US MD programs are rotating there, most likely the teaching is solid.
8. Don't be scared of scut, be scared of unrewarded scut. If the scut is rewarded with good teaching it is often worth it.
Hope you find this helpful. Good luck in 3rd and 4th year.