It takes several minutes to take the Yamanote line to Akihabara from Tokyo station. I walk there sometimes from Jimbocho or Ochanomizu. It was once world famous as the electrical town, however, it is changing to the PC town and the area is expanding. And now, it is changing to anime-otaku city.
I mention Shosen Book Tower as a bookseller I visit when I come to Akihabara. It has full of electric, electronic, informational and PC related publications or a little nerdy ones as is expected from the place. If you want other kind of books, you had better go to Jimbocho or Yaesu.
As for computer or PC books and magazines, there are hot-selling ones in Laox. It moved from the first floor of the Computer Kan to an annex building, Shoseki Kan, but the bookstore moved again to the top floor of the Computer Kan (Update: 2003.11.16). It has a best selection of the PC books. You can visit after closing of other booksellers because it is rare to be open till 9 p.m. in Tokyo metropolitan area. It is a PC shop that is the largest and reliable in Akihabara --- it is a rare shop that keeps information on compatibility of PC peripheral devices. (Update: 2001.12.30)
When I look for electric or electronic publications, I also visit a shop under the railroad bridge near the station or one on the second floor of Radio Department Store. They are small bookseller, but they keep the point. When you ask something, they will take it out from the back.
There has been getting many shops on game, animation, figure and coterie magazine recently in Akihabara. I am sorry to say that I don't grasp them even if they are booksellers. I hope you will not take it amiss. I guess larger shops are, for example, Laox ASOBITCIY, Animate, Toranoana, K-BOOKS, Kaiyodo, Hobby Base Yellow Submarine, maybe? (Update: 2003.11.16)