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LABYRINTH BOOKS (112th bet. B'way & Amsterdam) is the largest scholarly bookstore east of the Mississippi. It's rather spartan in appearance, but it does systematically stock highbrow reading material in the usual disciplines. If you want a copy of Plato to peruse in the original Greek, or anything deconstructed, this is the place. Mediocre magazine selection, not strong on the arts.
THE LAST WORD (118th & Amsterdam) is a rambling used bookstore that will buy your odds and ends. Adequate selection heavy on old favorites; still not the Strand.
LIBERTY BOUTIQUE (113th & B'way) is a locally-owned treasure of a clothing and accessories store that has no relation to the famous store of similar name in London.
COLUMBIA UNIVERSITY BOOKSTORE is a serious bookstore in its own right, with a specialty in faculty authors. Loads of school supplies; oodles of Columbia trinkets.
GLOBAL INK is the good, locally-owned, magazine store. It is the mortal rival of Universal News across the street, a chain rival that opened there in a snit because Columbia wouldn't give them the space. Pastries and coffee in addition to obscure and wonderful magazines from around the world.
MONDEL'S CHOCOLATES is sublime. This locally-owned shop of hand-made candies will ruin your appetite for your real dinner. Simply to walk inside for the smell is worth it.
JANOFF'S STATIONERY is a longtime neighbor with a small but expert selection centered on paper goods and implements for writing on them.