I have few recommendation.
Taiyaki is something like a pancake, but fish shaped and has red bean paste inside. Usually, it's best to eat when it's freshly baked. However, eating hot Taiyaki in summer may be hard sometimes.
There is this famous place called "Hiiragi" in Ebisu. At Hiiragi, you can try Taiyaki dipped in a cup of soft serve! It's limited only during summer.
It looks like this: https://www.instagram.com/p/BHbpqWuhHye/
You can find this at Nakamise-Dori, a shopping street connected to Sensoji temple in Asakusa. This is a deep fried bun with red bean paste inside. It's crunchy outside but soft inside. Perfect for a snack if you stop by Sensoji temple.
3. Anmitsu / Cream Anmitsu
Speaking of Sensoji Temple, there are many Japanese cafes around Sensoji and Asakusa district. Most of those kind of cafes offer "Anmitsu". It's a cold dessert with "Kanten", transparent jelly-like cubes made from vegetable galatin, fruits, and red bean paste. "Cream Anmitsu" has a scoop of vanilla ice cream or soft serve on the top :P
If it's during hot season, "Kakigori" and "Warabimochi" are recommended!
Both of them are standard of Japan's summer dessert.
Kakigori tastes quite different depending on the restaurant.
"Himitsu-do" in Yanaka is recommended. "Strawberry milk" is a standard there.
The place is so popular that you will need to line up on weekends.
Himitsu-do often closes early, so be careful.
Another famous Kakigoori shop is located in Roppongi.