My German friend who is food photographer andrecommended "Ecole Levain D'antan" near Roppongi (http://ecole.landemaine.me/about/company#com04). He said the restaurant in Paris offer their bread. In case, you're not stick to Japanese one.
I like Gontran Cherrier. They have shops in Shinjuku, Shibuya, Nihonbashi, etc. Their croissant is the best!
Dominique Ansel Bakery is also very popular now in Tokyo. They have many unique breads such as the shape of Onigiri (rice ball)
Another one I'd like to recommend is "Bread, Espresso &) in Omotesando. Their bread is so soft and fluffy. French Toast is famous but it is only available at the cafe from 3:00 PM and the cafe is always crowded, you will have to arrive early and wait in the queue.
FACTORY in Kudanshita has the best bagel. This bakery is very close to Yasukuni Shrine.