Whisky lovers are truly spoilt for choice in Tokyo. Aside from the great number of department stores in the metropolitan area that stock a satisfactory range, neighborhood districts equally have an abundance of dedicated shops that will not leave you disappointed. One particular establishment, naturally not new to the blogosphere, and which appears to be frequently visited by locals (a quick google search indicates this), has a very impressive selection of not only whisky, and all other worldwide spirits, but as well, there is a premium selection of craft beer. Tanakaya is a basement shop that caters to everyone's individual needs whether, you're after fine cognac or armagnac, limited rum or vodka, microbrew beers, and naturally independent whiskies. The shop, which is conveniently located literally a minute away from the Mejiro station, has a clean interior and layout that provides great browsing/shopping (liquor types are cleverly displayed in sections).
The Scotch whisky line-up (independents, limited releases, rare and vintage) is fulfilling and will not leave you displeased. However, currently the store seems to be lacking in Japanese whisky. On my visit only half a dozen bottles of On The Way, a bottle of Ichiro's Malt 23yo cask strength (original label), and a few bottles of a private release Akashi 5yo could be had. For those looking for standard expressions, i.e, Suntory and Nikka, perhaps you should look elsewhere - it appears Tanakaya do not stock official bottlings from the giants. Perhaps the store has so much traffic that any limited Japanese whisky that comes in goes straight out, a "need to be quick" policy? Well worth a visit regardless, and don't forget to check out the beer fridges, hard not to really. A classic liquor shop indeed.
Access: West of Mejiro Station (JR Yamanote line)