Maruzen in Marunouchi
Maruzen is one of the big bookstore chain with Kinokuniya.
The one in Marunouchi is in Oazo building, 20 meters away from Tokyo station Marunouchi North exit.
They have everything you would want: all kind of literature, and also a huge collection of art and science, including economics and business, cuisine, travel, philosophy, education books, all the major newspapers and magazines. They even have Paris Match! the people magazine that is soooo necessary to all of us.
Maruzen is also a partner of Amazon.jp so if you cannot go to Tokyo, you can still do some online shopping in the english book section!