I've shopped quite a bit in online bookstores.
Online Japanese bookstores are expensive.
They don't ship overseas, except these three:
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 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.