Shinjuku is the heart of Tokyo. It's probably the first place people think of for nightlife, shopping, and dining, really without leaving the station proper, but make sure you walk around. Take the Kabukicho exit out of the station and walk around the that area.
My favorite bookstore Kinokuniya is there, 9 or 10 stories of books. The comics and manga sections is massive. I am not a manga geek, but it's growing on me. It's good for my Japanese and the artwork is pretty cool. I used to think it was only for pervs, but some of the stories are really amazing. I love the size of the books. They are designed to be read on a packed train...