Quad Sports is certainly one of the best card shops in Japan.
In the very large store, there must be at least 200 monster boxes full of base cards (not all shown, of course), including NPB, Japan soccer, MLB, NBA, NFL, and idol cards. The best cards are in the showcases, which hold hundreds of autographs and relics, parallels, and more. Inserts are stored in binders in the cabinets behind the photo.
The older BBM card selection is pretty good too, though when it comes to pre-2000 cards, it can be hit or miss, though set selection still seems to be better than any other store I've seen yet. And of course, some sets have been stripped of most of the best singles by now. I believe a small handful of stars have been pulled out of all of the older sets, and they might be stored elsewhere.
The only real drawback of the store, though, happens in the organization of these sets. All of the boxes are labeled in Japanese, and boxes are stacked three high, plus two 1.5-meter (about 4.5 feet) stacks (and growing) of boxes that don't fit on the shelves. Getting to the right set requires a bit of Japanese knowledge. Older sets are a bit unorganized due to handling by customers, with early-90s BBM sets having major card-locating issues due to originally being sorted by team, not card number.
I only looked once or twice in the MLB boxes. Card prices are generally as you'd expect in Japan, overpriced compared to the US. However, I recall seeing a few cards priced at only 10 yen (10 cents) each. These boxes are sorted by player/team, and thus are really only useful for player collectors.
Quad Sports doesn't have a website as far as I know, and I'm not really sure when they're open, but they seem to hold at least standard hours and they're open on Sundays and Mondays for sure.
English here is really good for a store in Japan, and the guys who work here can answer most basic questions. They're pretty friendly and recognize me; they even have a basic idea of what I'm interested in when I visit and have shown me the latest product if it's not on the shelves/in the binders yet.