There are some zines, poetry chapbooks, and the like in the back of St. Mark's Books. Back, back past the service counter across from the magazines, back, back through the books and on a little stand-alone pillar stand of some sort. Just a few titles, just a few copies of each, mostly on consignment.
GRNY -- the local Giant Robot store -- also sells zines, if I remember correctly.
This is a good list to make. Gone are the days of Tower and See Hear, the latter of which closed in 2003 or so.
I also forgot, Forbidden planet on like 14th st? (across the st. from the movie theatre @ union square. Near Strand) has a good number of zines. Mostly comix but I've seen doris and a few other microcosm publications there.
Rocketship on Smith St in Brooklyn (the Bergen St stop on the F train) carries comics and zines that either pertain to comics or have a lot of narrative illustrations. The owners, Alex and Mary are incredibly nice and honest to boot.