Urban Center Books

Located in the leafy courtyard premises of the Villard Houses (the storied, long-time home of publishers Random House), Urban Center Books is a jewel box of books and journals on architecture and design. Stacked to the ceilings with nearly impossible to find titles, this airy, be-laddered shop turns browsing into a visual education. Plus: Urban Center events will put you at the center of discussion on architectural matters in the city.

Skyline Books

While their massive neighbor has shuttered its windows, Skyline continues toward the 20 year mark, "offering the book-buying public everything from inexpensive, second-hand reading copies of their favorite classics to high-end, rare, signed, and out-of-print titles."
If you're looking an atmosphere and inventory strong on Beat lit., this is your place.
Plus: Looking for some hard-to-find jazz vinyl to go with your Kerouac first edition? Academy Records & CDs is across the street, where you can chat with grade A music nerds about the strengths and weaknesses of various 50's sound engineers.

Mercer Street Books

Mercer Street Books is a classic New York used bookstore. A beautiful disaster of piles and piles of used, rare, and review books crowd nearly every bit of space in this nearly 30 year old shop, and yet those who work there seem to have a very good grasp on the inventory. Just don't hold it against them that a scene from the Drew Barrymore/Hugh Grant fiasco "Music and Lyrics" was filmed there. Plus: LP's!

Argosy

Argosy Book Store in Midtown has 6 levels of used and rare books and prints, as well as a great bargain table right in front of the shop. Strong on Americana, modern first editions, autographs, art, antique maps & prints, and the history of science & medicine. Plus: a fantastic wall of Selected Reading right as you walk in; a great place to find what you didn't know you were looking for.