I've shopped quite a bit in online bookstores.

Online Japanese bookstores are expensive.

They don't ship overseas, except these three:

• amazon.co.jp
• bk1.jp
• hmv.co.jp

Book prices seem to be fixed, so you should look into shipping costs and service quality in order to choose where to buy from.

amazon.co.jp and hmv.co.jp have English versions whereas bk1.jp doesn't.

I've bought from bk1.jp and hmv.co.jp.

amazon.co.jp has a marketplace where used books are sold. These can be much cheaper than new books, but they only ship within Japan so you'll have to use a forwarding service and do some math to check if what you are saving in the book's price is more than forwarding fees.