As I see it, there are about four ways to buy Japanese baseball cards in the United States:
1. eBay - eBay is probably the best place to find Japanese baseball cards although it is very inconsistent - you never know what you're going to find. And, of course, in many cases you have to deal with the frustration of being out-bid on something. But for volume and variety, it's tough to beat what's out there on eBay.
One suggestion that I would make - if you buy something from someone who is actually located in Japan, ask them if they are interested in selling other items to you. You might be able to set yourself up with someone who is willing and able to go to a card shop in Japan and find things for you. I've had this happen twice now over the years - the first was with an American who had access to a military base so we could ship stuff to each other via US mail, the second was with the Japanese gentleman that I get my sets from now.
2. On-line Japanese card shops - there are two of these that I'm aware of that will ship to the US - AmiAmi and Rakuten Global Market. Pretty much all you can get from these are new, unopened boxes of cards. I've ordered a bunch of box sets from AmiAmi without too much trouble (although they appear to sell out of stuff quickly) and they offer both EMS and SAL shipping. I've only ordered a couple of things through Rakuten - I could be wrong but it seems like they only offer EMS for shipping which can really run you.
3. US card dealers - the big US card dealers are Rob's Japanese Cards and Prestige Collectibles. Rob's is run by Rob Fitts who is focusing more on writing great books about Japanese Baseball history so the business is focusing more on older cards than on current cards - although I think he gets in at least a couple of the BBM 1st and 2nd Version sets each year. Prestige Collectibles used to be run by Gary Engel, author of "The Japanese Baseball Card Checklist And Price Guide" but is now owned by Robert Klevens, another of the Japanese Baseball Card "pioneers". Prestige Collectibles also runs auctions every so often with a lot of very interesting vintage stuff. I wouldn't necessarily take what's on the two websites as gospel for what either of them have in stock - if you're looking for something specific, ask them.
4. Auctions Yahoo! Japan via kuboTen. kuboTen is a proxy service that will bid on auctions on the Yahoo Japan site for you. There are fees associated with this and you'll end up paying for shipping twice - once for the seller to ship the item to kuboTen's office in Fukuoka and agin for kuboTen to ship the item to you - but a lot of times you can find great stuff fairly cheap on Yahoo Japan. Be patient with kuboTen, however, as it's a one man show and Craig has been known to get overwhelmed at times.