There are also regular fairs at the Holiday Inn around 52nd Street or so off Columbus Circle, I was there a few weeks ago and got a few decent albums at nice prices. Few boxes of unpriced 45's well worth going through if you have time, but not full of bargains and as has been suggested already well picked through. Goldmine will have dates.
If you need some new cartridges, stylus, mixers (!) etc get to 'Rock and Soul' behind Maceys they also have a fair few 70'/80's albums to browse.
Halcyon in Brooklyn on Water Street is ok if you are near by and its a good view of Manhattan from the Waterside, nice ice cream too !
What I found disappointing was the lack of new house 12's out on the shelves, Dance Tracks has shut and so has Satellite that used to be on The Bowery.
When in Greenwich Village get some Pizza from the shop at the junction of Bleeker and Carmine.
Enjoy your trip