There are several bookstores in Tokyo that are handling books in English, however, I think they are not carrying so wide range of books except language and literature.
I'd recommend Amazon.co.jp. They are offering many books and if the purchase amout is more than JPY1,500 they do not charge delivery fee. 洋書 Electrical & Electronics Books | Amazon
*If you click one of the books and then you'll find a message in the right top saying "Would you like to see this page in English ? Click here."
Once you click it, most of the information are shown in English.
There's a used bookstore called the Blue Parrot in Takadanobaba. Not far from the station. Not sure if it has IT books, though. I'd post a link but I don't think I'm allowed to.
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