KURAND is a bar type restaurant where you can try over 100 kinds of sake with a fixed price: ¥3,000. I have never been here but seems like a great place to try out various labels of sake. They have several branches in central Tokyo. The link below is Shinjuku branch.
Kuri in Ginza is a Japanese sake bar. They have 6 glasses course where you can try 6 kinds of Japanese sake selected by the sake specialized staff. They are offer mainly sake but specialized in Japanese drinks. So they also offer Japanese beer and some liquors and plum wines.
Recently, the international famous sake bran Dassai opened a flagship store in Ginza. They do not only sell famous labels of Dassai but also Dassai chocolate, Dassai Baumkuchen, etc. It might be an interesting way to try Japanese sake!
If you are in Tokyo, you can try to visit Kirin Yokohama Beer Village in Yokohama or Suntory Musashino Brewery in the suburb in Tokyo for beer.
And Ozawa brewery for the sake; you can learn everything about sake there. They have the museum too. You can stay there all day! Here is the info: http://www.sawanoi-sake.com/en
Kizakura Fushimigura in Kyoto was opened last year, they have a brewery for a beer and a brewery sake!
Like most of the Japanese breweries provide a free tour and tasting, and you can learn everything there!