My favorite bakeries in Tokyo are below.
- Gontran Cherrier Tokyo
Has the best croissant I think in Tokyo! The branches are in Shibuya, Shinjuku, Nihonbashi, etc.
Is located near Yasukuni Shrine. They have the best bagel.
- BOULANGERIE Le'crin
Has the best baguette.
- Kagawa Ichifuku
Ichifuku got a Bib Gourmand on Michelin Guide 2017. My favorite is "Bukkake Udon" but other person said "Curry Udon" is the best.
It's in Shinbashi or Gotanda, they don't have English menu but the Udon is very good, chewy, and tasty!
I will leave cafe and ramen to other people :)