In Akihabara the bookshop with the best collection of new books and magazines is "SHOSEN BOOK TOWER", especially their 5th floor with all the latest and older modelling/history releases. Get out of the Akihabara station from the "Showa Street Exit" and turn right.
Choosing "Yamanote Line" to move around Tokyo, there are three important stops to remember: Ueno, Okachimachi and Akihabara. Ueno is a must because of all the museums, the zoo and the Ueno Park with Shinobazu pond around where you can enjoy the beautiful cherry blossoms if the season is right. If you choose to walk from Ueno to Akihabara (about 15min fast pace) there is the always exciting Ameya-Yokocho market (usually called "Ameyoko") between Ueno and Okachimachi stations, and the "NISHIYAMA Bookshop" that specialises in modelling/history books in every language except Japanese. It used to be in Ikebukuro but relocated very recently. It is one of the very selected spots around Tokyo where Arawasi publications are available.
It is close to "Leonardo's" and "TamTam", as you can see in the map, so it is definitely worth the while to pass by for a close inspection.
This posting will be updated with photos and addresses so come back again for more and don't forget to take a look at Pt#1 for updates.