If you're on the hunt for a particular craft nihonshu (sake) and shōchū (distilled liquor usually made from barley or sweet potato), zone in on this off-the-beaten-track liquor shop. Run by the same family for over 300 years, it stocks around 2000 different labels.
There's usually someone available who speaks some English and can help you pick something from the selection. Its Naka-Meguro shop has a counter bar where you can order nihonshu by the glass (around ¥500).