I couldn't make it to every single bakery, but here are the places I went to, and in the order of my personal ranking.
Meilleur Ouvrier de France
THEE BEST CROISSANT I have ever had. There's nothing more to say. You just have to try it.
Des Gâteaux et du Pain
The second best place I have tried, and they have a big variety of pastries to choose from.
Gérard Mulot
Good pastries with a lot of gorgeous desserts.
Du Pain et Des Idées
Fine bakery with traditional décor.
