The number of Japanese whiskey bottles are getting less and less due to the popularity of whiskey in past few years, and it is becoming harder to encounter to Japanese whiskey with "aged" labels at bars nor stores. However, these bars might have such bottles:
Brilliant in Keio Plaza Hotel
There might be a higher chance to encounter aged bottles of famous labels such as Yamasaki or Hibiki at bars in hotels.
Nikka Blender's Bar
This bar is located under the headquarter of Nikka company. You can try various NIKKA whiskey here.
Others are listed here:
If you have a chance, visit one of the distilleries!
How about the Tokyo Whiskey Museum? You can try more than 1000 kinds of whiskey from Japan and all over the world! The only the whiskey, but the appetizers are also wonderful! Try it out!