Ginza has surpringly few good foreign language bookshops. Book 1st has opened a branch at the 6th floor of "Ginza Core" (5-chome), between Matsuzakaya and the Nissan Building. There is a small English section, as well as a few international magazines and newspapers.
Otherwise, Asahi-ya in the Sukiyabashi Hankyuu Building (look for "Gap") also has a small selection of English books (mostly travel-related).
Tokyo station, Otemachi, Nihombashi
In this area (what some would call the "center") you'll find, in order of importance :
Yaesu Book Center, in front of Tokyo station. 7 floors, the last one for foreign books. It's a bit old. There are no lifts/elevators and escalators only go to the 5th floor, but the choice makes up for it.
Maruzen (丸善), has just moved to the new OAZO shopping center between Marunouchi and Otemachi. Only 4th floors of books. The selection of foreign books is one of the best in East Tokyo.
Kinokuniya (紀伊国屋), in Otemachi, inside the Otemachi building (ground floor). Just one floor, but at least there are English novels and the last bestsellers. You'll also find LP guidebooks and magazines.
JTB's Ryo no Toshokan (旅の図書館) is not a bookshop but a library. All the books are travel related and a few hundreds of them are in English, including many Lonely Planet, Let's Go, Michelin and Blue guides. It is located at the basement of the Tekko Building No 2 (第2鉄鋼ビル, near the Yaesu North Exit of Tokyo Station. The library is open Monday to Friday from 10am to 5:30pm. Entry is free. Don't forget to leave your bag(s) in the lockers (you need a 100yen coin, but it is returned afterwards). Photocopies of any book can be made for about 30yen per copy.
Kanda-Jimbocho
This is the Book district in Tokyo. They are too many bookshops to cite them all. The largest and most likely to interest foreigners is Sanseido (三省堂). It's on the Yasukuni Dori (靖国通り), just in front of the intersection of Meidai-dori (明大通り), leading to Ochanomizu and Meiji University.
Shinjuku
In the busiest part of Tokyo no need to say you'll find what you want. My first recommendation goes for Kinokuniya (紀伊国屋). There are 2 branches. The best is the one behind Takashimaya-Times Square. The other one is in near the Shinjuku 3-chome underground exit (on the street of Isetan, Marui, etc).
Shibuya
Shibuya's Book 1st (ブックファースト) is one of the best deserved bookshop of the capital for foreign books. You can't miss it, it's on Bunkamura Dori, 2 minutes walk West from the station.
Ebisu
Atre Department Store's 5th floor Yurindo (有燐堂) has a small bookshop with a few English books (travel, dictionaries, English teaching, novels) and magazines.
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