Used: "Good Day Books" in Gotanda/ New: "MARUZEN" in Otemachi
If you would like to buy a used English book, I recommend "Good Day Books" in Gotanda which is 15 minutes from Tokyo station on the Yamanote line. This book shop has various kinds of books. Check the map:
If you would like to buy a new English book, I recommend "MARUZEN" in Otemachi. I really like this bookshop's atmosphere- I feel comfortable and relaxed with many books in organized book shelves.
Here is the map: