well, i attended both hunter and nssr, the former as an undergrad (and later took some grad classes) and the latter for my MA. i wasn't particularly fond of the ma program at hunter, with the exception of the classes that were cross-listed w/ the phd program at the graduate center. the program seemed pretty poor on the advising front. the grad students i knew there were not assigned advisors when they entered the program. it was up to them to find them when it came to thesis writing time. it's also a 4 field department, so be prepared to take requirements in bio, ling, and arch too. in comparison, new school is strictly socio-cultural. i found the program to be pretty theory heavy, which I thought was useful. that said, the funding is *terrible* and the best professor in the dept (hylton white) just left. i had planned to stay on for the phd, but decided to apply elsewhere b/c of the funding. yet, having my MA from there opened quite a few doors for me, at least i think it did. anyway, nssr does admit quite a few students to the ma program, but not all are accepted into the phd program, so i don't think the quality of the program suffers from the number of students. also, all the folks in the dept are well respected in the field.
hope that helps.