Hi there !
If you are just looking for books - you can find them in any bookshop in Tokyo - go to the hobby shelf - or ask for assistance from any of the clerks (usually faster than looking for it yourself) - tell her you are looking for "amigurumi no hon" (means "amigurimi book).
Each bookshop stocks its own selection of books (personally selected by the shop manager based on the stats and interests as well as what sells in the area or location of the bookstore) so you don't usually find all the published books in one bookshop. You may need to visit several bookshops. Also you need to know that bookshops usually stock only the recent publications (usually appropriate for the season)- if you want something published last summer or 2 summers ago - it might prove impossible to find much less get.
So if you have certain books you want - it would be good idea to list down the ISBN numbers (Name of Publisher also and maybe the title of the book) before you come to Japan - if you can also take photos of the book covers - it will help a lot.
If you are looking to get some supplies also - you have to go to a craft shop... see this post for more info on the craft shops in Tokyo - http://www.craftster.org/forum/index.php?topic=127214.0
Some crafts also stock some books and if you are lucky you might find some of the older publications in their shelves.
Hope this helps... Good luck.
Enjoy your visit to Japan and have fun.