score:6
I just happened to stumble over an article in Time Out last year about the Craft Beer scene in Tokyo - managed to find it again with some creative Googling: Time Out Tokyo: Craft Beer In Tokyo. One of the articles at the bottom of the page lists Tokyo's best craft beer bars. From a quick skim, it seems most are bars that serve craft beer, not clear if there's much in the way of actual breweries you can tour or microbrewpubs.
Upvote:2
Ryujin Shuzo Brewery (or Ginko Kura Brewery) from Tatebayashi, Gunnma Prefecture, is about 80 km far from the capital Tokyo. Oze no Yukidoke IPA (that I tasted) seems to be their most popular beer but they also brew two kinds of sake (source).