Before I actually moved to Japan, the only places I ever knew of to buy baseball cards was at the baseball stadiums themselves, at the team goods stores. Now, living here and being an explorer in general, I've found lots of other places to buy cards, which is great. (My wallet disagrees with me, but whatever.) A few of these places in the Tokyo/Kanto area are:
The Sports Authority. The ones near me generally stock a lot more soccer goods than baseball goods, being as I'm in the same prefecture as the the Urawa Reds, but they'll have some baseball card packs lying around as well, usually just the current BBM set and maybe a few assorted team packs, plus some MLB Upper Deck packs and the like. They also usually have a whole bunch of Japanese player MLB goods (think Matsuzaka jerseys and jackets, or Yankees hats or Ichiro shirts) and not much in the way of NPB.
Yamashita Shoten by the Tokyo Dome.
Tokyo-to, Bunkyo-ku, Koraku 1-3-61 Kiiroi Building 2F
This bookstore is between the Tokyo Dome and Suidobashi JR station; from the Dome go down the walkway and stairs opposite Gate 23 and it's on your right before you hit the videogame arcade. They stock a ton of sports magazines and books in general and about 10 different types of baseball card packs (some team packs, some things like the Nostalgic set, then Rookie Edition and Back to the 70's, plus random things like Giants 2005, and they'll usually get in the boxes like the All-Star set, the Nippon Series set, the Furuta retirement set). This is also a pretty decent place to pick up monthly baseball magazines for various teams and leagues. I have an almost-weekly routine of going to the Tokyo Dome shop to look at team goods, then stopping by nearby Yamashita to actually get magazines or cards.
Shosen Book Mart in Jimbocho.
Tokyo-to, Chiyoda-ku, Kanda Jimbocho 1-21-6
From Ochanomizu JR station, take the "Ochanomizu Bridge exit" and walk down the hill away from the river. You'll go through a whole ton of guitar shops, and then Meiji University will be on your right, and eventually you get to Yasukuni street; Shosen Bookmart is across the big intersection from you at that point. Go into the basement; near the entrance to your left you'll find various card packs (mostly team packs, plus last time they had some 2006 BBM 4-card sets for 100 yen each). In the back right corner there's also a ton of baseball books and magazines, including many "new" copies of "old" issues of stuff. Fantastic if you want things like a 2006 Japan Series program.
(As an aside, there is a used book store in Jimbocho called @wonder that has an AMAZING wall of old NPB books and magazines, including Shukan Baseball going back over 30 years, other old magazines and team books and whatnot. It is practically next door to the Jimbocho subway station exit A1, on Yasukuni Street. Tokyo-to, Chiyoda-ku, Kanda Jimbocho 2-5-4)
Most other major book stores actually will have baseball card packs somewhere, if you just know where to look. This includes Kinokuniya (the large 8-floor Shinjuku branch has them on the 6th floor to the left of the cash registers; baseball books in general can be found in the front left corner of that floor) or Sanseido (the big store right across from Shosen has some packs by the escalators on the third floor)
R&B21 in both Ryogoku and Shinjuku (and Osaka!)
Ryogoku store Map: Tokyo-to, Sumida-ku, Ryogoku 4-37-2
Shinjuku store Map: Tokyo-to, Shinjuku-ku, Nishi-Shinjuku 7-1-7
This is a really interesting store. They don't really have much in the way of Japanese baseball cards or packs or anything, which is kind of funny, but they're your place to go to if you're living in Japan and looking to buy or trade MLB cards, or football/hockey/basketball/etc. They make their very own patented thick card holders among other things. The people there are really nice, but they don't always have someone around who can speak English, which is odd considering their stock. However, if you're interested in their card holders, they can do English over email, and they're happy to ship them to other countries, and you can pay via Paypal and such. The above links are English directions to their stores, and I can at least vouch that the Ryogoku ones are valid.
I've bought things from all of the aforementioned places, but the real inspiration for writing about this is a store called Mint, which I have spent way too much time and money at in the last few weeks. See, most of the places I've listed here that sell NPB cards basically have them in packs. Mint is awesome because you can just go in and look through individual cards for hours and hours. Not that I've done that, of course... anyway, next post is going to be just about the different branches I've visited of the Mint store chain.
Let me know if this information is actually useful to anyone. I'll try to organize it better later.