I think the Strand is worth checking out, although I go there infrequently. It's more like a junk shop for books - lots of titles, but you don't necessarily know what you'll find.

My personal favorite bookstore in the city is Book Corner on 112th east of Bway. It functions as a semi-official Columbia bookstore, but they have an extremely comprehensive fiction section. They also have an excellent collection of foreign-language books (for my purposes, Spanish and French), and that's my primary reason for shopping there.