For traditional Japanese confectionaries there is Toraya, which is one of Japan’s most famous shops with locations around Tokyo. A modern confectionary shop that I love is Higashiya in Ginza. I first met the folks from Higashiya at a food event where I was pouring dessert wine from Coco Farm and Winery. The Higashiya team were serving wagashi with shochu. I knew immediately that they were worth exploring and I have always been delighted with the sweets from Higashiya.
The Ginza shop is conveniently located in the heart of the shopping district, so a good excuse to rest your feet here and to rejuvenate over some sweets, either traditional or modern. Check out the mattcha blanc manger or the houjicha pudding or for something more classic, the monaka or yokan.
Chuo-ku, Ginza 1-7-7, Pola Ginza 2F