Most tokyo whiskey bars are tourist traps charging ¥3000 for a shot. But a few places are legit.

Bar high five in ginza - the bartender knows his stuff and the selection is insane. Expensive but worth it for special occasions. Bar benfiddich makes their own bitters and has japanese whiskeys you can't find anywhere else.

Skip anything in golden gai for whiskey - they're beer and sake bars that happen to have bottles on the shelf. The real whiskey culture is in quiet basement bars in ginza and shibuya.