****JAN 2014 UPDATE ****
For more in-depth and recent information on actual physical card shops in Japan, visit This Card Is Cool for locations and experiences at several shops.
I asked around on a couple of sites about whether there were any good online cardshops in Japan, but didn't receive any responses that didn't involve American sites selling Japanese cards. So, grabbing some keywords from my various Yahoo! Auction Japan searches, I set about digging for some sites I could order from using KuboTEN.com. As of yet, I have not ordered from any of these, so your mileage may vary. Most of the sites I found sell baseball (both NPB and MLB), soccer, wrestling and several other sports and non-sports. I'll post both the native links, as well as the Google Translate versions.
http://mint-web.jp (Mint Web in English)
Mint is a franchise of collectibles stores carrying all kinds of stuff in addition to just sports cards. There are several stores scattered across Japan. While they apparently have a very large, and at times very cheap, inventory in-store, the website doesn't seem to have that much for sale outside the most recent products. You can read about them on Deanna Rubin’s blog: http://marinerds.blogspot.com/search/label/Baseball Cards
The following I found in the classified ads at the back of the latest Sports Card Magazine that is produced by BBM (Baseball Magazine) mainly as a price guide and advertising vehicle for their own product.(though they do list a few other current sets from other manufacturers, mostly they just cover BBM):
http://www.e-bits.net/ (Sports Card Bits in English)
BITS! almost doesn't need the translation, as most of their graphics are already in English. They offer boxes, packs and singles (BBM back to 2004 and Calbee back to 2007).
http://www.cardfanatic.co.jp/ (Card Fanatic in English)
Card Fanatic seems to revolve mostly around American cards and cards of Japanese players in America. Probably not of much interest unless one just feels the need to pay an extra $50 per box for something that is readily available from Blowoutcards.com or any other online American card shop.
http://www.rakuten.co.jp/cardya/ (Cardya in English)
Good luck with this one. Lots of their graphics and buttons are in Japanese, so the online translators don't work. There is a player/team search near the middle of the page, though.
Yes, that's Amazon's site in Japan. Much the same as they are now beefing up their individual baseball card listings through their partnership with several dealers and CheckOutMyCards.com, the Japanese site also has thousands of single cards listed.
Mentioned quite often on the Japanese Baseball Card Blog, AmiAmi is one of very few online Japanese stores that has an English site and does sell and ship internationally. NPBCardGuy orders lots of smaller sets and recent boxes from there. Describing themselves as a "Character & Hobby Shop", AmiAmi carries an enormous stock of figures/statues of all manner of Japanese characters, as well as a fairly decent assortment of current unopened boxes of trading cards, both sports and non-sports. It's basically a fully stocked Japanese comic shop with a few extras.
6 hours ago