If you are doing research on Japanese film, a constant bother is not only the lack of available films, but also the paucity of books and magazines. Literally thousands of books and magazines on cinema have been published in Japan, but few have been collected outside of Japan and even Japanese libraries, not having considered film studies a legitimate institution, often have surprisingly poor collections. That is one reason why I spent several years in Japan scouring through used bookstores to build up a sizable collection at the University of Iowa. But even if such books are available through interlibrary loan, a book in hand is better than two at Iowa, you could say, so many people visiting Japan ask me where they can buy books on film. This, then, is my spiel on film specialty bookstores in Japan.
Books on film still in print can certainly be found at most any sizable bookstore in Japan, but some are better than others. In Tokyo, the Yaesu Book Center near Tokyo station is probably the best stocked, but Libro under the Sezon Museum of Art in Ikebukuro, or Kinokuniya in Shinjuku also have good selections.
The only new bookstore almost totally devoted to film is the Bungeiza Cine Boutique on the first floor of the Bungeiza Theater in Ikebukuro. It not only has a good selection of new books, it has some monographs that are technically out of print, film pamphlets, privately published fan magazines, festival catalogs, and some back issues of film magazines. Definitely worth a visit, especially if you are going to catch a new or old film at the Bungeiza.
For out-of-print books, or for new books at lower prices, there is always used bookstores, of which there are thousands in Japan. Luckily, a few of them handle quite a few film-related books. When you are in Japan, you can always visit them or go to one of the many book fairs in which they participate, but if you are not, some, like Kimoto Shoten, publish catalogs through which you can mail order books. Here are a few of the film-speciality used bookstores.

A short walk from the Itabashi Station on the Saikyo Line, Kimoto Shoten is a used bookstore that specializes in theater and film books and is one of the better places to find runs of old magazines. With a branch store/warehouse not far away, their stock is considerable. The catalog they publish is very helpful and, while books may seem pricy, that's what you pay for this kind of collection.
6-86-15 Takinokawa, Itabashi-ku, Tokyo 114
Inagaki Shoten may seem small and out of the way, but with an owner very knowledgable about film, it is one of the better places to find especially prewar film books. Just turn left as you exit the Mikawashima Station on the Joban Line: it's about a 100 meters away on the other side of the street.
3-65-2 Arakawa, Arakawa-ku, Tokyo 116

Probably the most well-known film used bookstore because of its location in Kanda, the used bookstore Mecca of Japan. Dealing with film and theater, they have put an effort into screenplays and have even published an index to published screenplays. Yaguchi is, however, also notorious for its unreasonable pricing, so while it may be worth a visit, let the buyer beware.
2-5 Kanda Jinbocho, Chiyoda-ku, Tokyo 101
A second option in Kanda is Book Power RB, which is devoted to sports and popular culture in general. They have an odd selection of books and magazines, television and film scenarios, and some collectors items like scrap books and stills. One unusual and helpful chore they are doing is organizing their programs in alphabetical order so you can actually find something you're looking for. This is also a good place to pick up film special issues in non-film related popular magazines, for which they have a surprisingly good selection.
2-13 Kanda Jinbocho, Chiyoda-ku, Tokyo 101
While they may not specialize in film, many other used bookstores have enough of a collection that they might have the book you are looking for.

The Waseda area with around twenty bookstores along Waseda Dori is another major used bookstore center that tends to be cheaper than Kanda and have more stores that carry film books. Especially check out Bunshodo, Kosho Gensei, and Arakawa Shoten.
Stores like Abeno Stamp in Kanda and Oi Stamp in Nishi Oi are some of the many that deal in film pamphlets and posters.
Everything mentioned so far is in Tokyo. While there are used bookstores outside of that metropolis that have film books, many I have unfortunately not been yet able to visit. One place I have been to that I can recommend is Kohon no Ogino in Osaka (4-6-8 Matsuzakicho, Abeno-ku 545), which is near the Fumi no Sato station on the Tanimachi Line.
Since I am perpetually on the lookout for good film bookstores, I would appreciate any additions to the above list people can offer.
Aaron Gerow