online stores selling Japanese craft books

Amazon Japan
Brian's Bookshelf has a very good guide to buying from Amazon Japan
craftlog guide to navigating Amazon Japan (including ISBN search)
Copper Coyote
Sasuga Books
Vintage Vogue (mainly quilting magazines)
Hakubundo (US store, will do special orders)
Whimbeads (a few beading books in the foreign books section)
Atelier Jade
The Paper Princess
Sasuga Books (not a great craft book selection, but will do special orders)
BraidersHand (a couple of kumihimo books)
Junku Librarie Japonaise (France)
Kinokuniya (US, Australia, Singapore, Malaysia, Thailand)
Liveria Fonomag (Brazil)
Saucylouise (also Etsy shop, based in Japan, ships worldwide)
Modern Craft (based in US, ships worldwide)
Felt Cafe (based in Japan, ships worldwide)
M is for make (based in the UK, ships worldwide)