Best depends on what you are looking for.

Are you looking for the best price? Or highest bandwidth? Or reliability? Do you need a static IP address (so that you can host your own servers)? Does best include customer support? Do you want support in English or is Japanese OK? Is the pipe to the Internet all you care about, or do you want other services, like email, web pages hosting?

What I did to choose my ISP was answer all these questions for myself, then bought a magazine that lists all Japanese ISPs: Internet Magazine. (I don't think you can find it in convinience stores, but it's available in book stores).

Note that Internet Magazine publishes a very cool and updated map of the Japanese Internet. It used to be a big poster, and looked really cool on an office wall. Unfortunately, now it's on a CD in PDF format, which is much less usable, and much less cool... but still very usefull to choose your ISP: if you are looking for bandwidth, you can just see how well an ISP is connected to the rest of the Internet. So you can realize that that unbelievably cheap ISP is just connected to the net by one tiny link. Also bad for reliability: if that link goes down, your connection may be down for days before they can fix it! On the other hand, you will find some ISPs that are connected to the rest of the Internet through multiple fat pipes. If you want reliability and bandwidth, go for one of these. But they are a bit more expensive...

So, if you tell us what you are looking for, maybe we can give you more precise recommendations.