Here's several: Midtown Comics near Times Square, Jim Hanley's Universe (around 4th West and 33rd Street), Forbidden Planet (a bit of a walk from 14th Street Union Square).
As long as you're in Manhattan, I highly recommend giving Jim Hanley's and Midtown Comics a visit. You can google them to find their exact location on a map.
Depending on what you're into I also recommend Toy Tokyo and Image Anime. IA is somewhere around 30th and 8th (been a while). Not sure if Toy Tokyo has relocated yet but you can google them too.
Haven't been to St. Mark's Comics in years but they used to be pretty good.