I depends on what kind of drinks you like..
If you like Japanese Sake, you can go to the Japanese style standing bars 'Tachinomi' .
Tokyo’s drinking scene is one of the best in the world.
Try these places:
Bar High Five
Geronimo Shot Bar
There are so many bars in Tokyo and different kinds!
If you are looking for authentic bars to have some whiskey or cocktails, Ginza and Shinjuku Sanchome are one of the top choices. You can find small bars.
For Izakayas (where is a type of bars enjoy drinks with foods), you can find it everywhere in central Tokyo such as Shibuya, Shinjuku, Ginza, etc. From big chain Izakayas to small private ones. There are many small and quiet Izakayas in Ebisu.