If you have one night in Tokyo and have malts on your mind, there is only place to go: Helmsdale (http://www.helmsdale-fc.com/
Despite the map, it is no easy to find, and the bar itself is very small and unassuming. On the shelves, however, is a staggering number and variety of malts, including several superlative SMWS bottlings and a full range of japanese malts. The prices are reasonable and you can get surprisingly good pub food there, as well. The closest train station would be Ebisu on the Yamanote line.
Suntory has at least one whisky bar in Ginza. The whisky is excellent, but the food is average and the prices are quite high.
If you know where in Tokyo you are staying, I might be able to recommend something close to where you are. Tokyo can be a bit overwhelming at first, and if you are jet-lagged you won't likely want to search around too much.