A major "craft" beer
Japan's readily available beers are all of the same light lager category; Kirin, Asahi, Suntory, and Sapporo. While there are slight variations in each, such as a black beer from each maker, IPA, stouts, etc are not easy to find. One beer however that is somewhat crafty that is conveniently available most supermarkets is "Heartland" beer, made by Kirin, always sold in characteristic green bottles.
This beer is still considered a lager, but has definite accents of an ale, providing for a richer and more filling drink. The brewery is actually located in Roppongi, a sort of central night life hub in Tokyo's downtown area.
Here is a link to the brewery: