I would recommend
http://www.bk1.co.jp/ for most of your Japanese book shopping needs. SAL shipping is very cheap (11 bucks for 1kg, see:
http://www.bk1.co.jp/contents/help/he-0201-04.asp), reaches your doorstep in about 1.5 weeks and you don't have to pay tax plus the book price is at retail price. Best of all it sends book vouchers to your email quite frequently (300 yen for min 3k yen u spend). For a Japanese novel I might have to pay 14 bucks at Kino. Via bk1 I would probably spend about 10 bucks including shipping.
BTW, book packaging from this company is fantastic, they really take care in protecting your books. If you're the nitpicker like me, skip Amazon.jp if you can because the packaging is quite atrocious (though still a lot better than Amazon USA)