Of course, any book in print can be ordered from any book store. However, if you want to browse for new books, there are a few that stock decent selections of film books. In Kanda, take the A7 Exit and walk down Yasukuni-dori away from Iwanami Hall and you’ll hit the following:
Shosen Grand (1-3-2 Jinbocho): They keep their film books down in the basement, and generally stock the more academic books that are hard to find in other stores.
Sanseido Shoten (1-1 Jinbocho): Has a good selection of scenarios and the last year of major magazines on the first floor.
Also try Kinokuniya in Shinjuku, the massive book store in the Ikebukoro Seibu, and the Yaesu Book Center near Tokyo Station. In Aoyama, Book City has a spotty selection of books, videos, and posters primarily on Asian film, as well as the recent runs of periodicals; they also have stores in Fukuoka and Sapporo.