To get a real “Japanese experience” I highly recommend staying in Shibuya or Shinjuku. They’re close to everything and the ability to walk out and see the energy of Hachiko or Kabukicho is really fun. Shibuya has a ton of construction and it can be confusing, but it’s a blast. These are all better than the relatively buttoned down areas of Shinagawa or Tokyo Station. With Tsukiji, I did the inner market 3 years ago and was pretty disappointed, but then did the outer market 2 weeks ago and it was a lot of fun.