Listed in alphabetical order!
Academy Annex - 96 N. 6th St. (Between Berry and Wythe) Brooklyn. I think this is considered THE place in NYC for general used vinyl.
Cinders Gallery - 103 Havemeyer St. (Just off Metropolitan Ave.) Brooklyn. They have great art shows, too.
Desert Island - 504 Metropolitan Ave. (Between Lorimer and Union) Brooklyn. New indie comic shop.
St. Mark's Bookshop - 31 3rd Ave. (at E. 9th St.) East Village. My favorite place to buy books when I'm not busy undermining small business efforts by shopping online.