To answer my own question, so far I’ve found:
http://www.wing-24.com
http://mint-web.jp/
Mint is a franchise of collectibles stores carrying all kinds of stuff in addition to just sports cards. There are several stores scattered across Tokyo. 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
Since there’s a space in the URL, for some reason the link doesn’t work, so you may need to copy & paste the address into your browser.
The browser title bar calls them the “Single Card Marketplace”
http://www.r-b21.com/singlecard/index.html
They sell a wide assortment of sports and non-sports singles.
---edit---
One more I’ve found is Mitchael Trading at
http://mitchael-trading.com/
Treasure Box - geared more toward trading card games, but that includes Konami’s products!
http://www.hobic.jp/