You can do your research before getting to New York:
Kurland Photo is at 670 Broadway, Suite 501 (two blocks south of 4th street), on the same floor as the Leica gallery. Craig is a gentleman and very knowledgeable. He used to work at Tamarkin. (Kurland is in Tamarkin's old location.)
Photovillage is on 1133 Broadway, Suite 824, a bit further up, at 26th street. Rich Pinto is a Leica legend.
B&H is on 9th Avenue, between 33rd and 34th street. They occupy the whole block, and their second floor is probably the biggest camera toy store I've ever seen.
Adorama is on 42 West 18th Street, between 5th and 6th avenue. (Note that addresses East of 5th avenue are labeled East, and West of 5th Avenue are West. Makes no sense, but good to know.)
Ken Hansen used to have a store, but now it's by appointment only.
You can do your research before getting to New York:
www.kurlandphoto.com
www.photovillage.com
www.bhphoto.com (click on Used Store)
www.adorama.com
Some of them also have eBay stores, so you can find things over there too:
http://myworld.ebay.com/kenhansenphoto
http://myworld.ebay.com/kurlandphoto
Note that B&H and Adorama are closed on Saturdays. B&H is usually packed with Europeans, it's a tourist destination for camera junkies.
There are some very sleazy stores (not the ones mentioned above), so if you stick to the above, you're in good hands.
If you find something online that you really want, you can call them and they will hold it for you until you get there.
I hope this is enough to get you going.
Best of luck!