Go to Shinjuku Kinokuniya Bookstore at TimesSquare
I guess Kinokuniya at Shinjuku TimesSquare offers the widest range of selection in terms of English books. Magazines, hardcovers, paperbacks, even Mangas in English, you name it! It is on the 6th floor and can be easily accessed from Shinjuku station. It even often holds English book sale which is not available with Japanese books since book pricing is regulated under Japanese laws. The store is usually open till 8:30 p.m.