Takano Fruit Parlor in Shinjuku provides delicious fruit parfaits! Their parfait using seasonal fruits are amazing. I am sure every children like their parfait.
Tsujiri in Daimaru Tokyo Department store (connected to Tokyo Station) serves great matcha ice cream. It's originally a tea shop in Kyoto.
Ginza Sabou has beautiful desserts using matcha and other traditional Japanese ingredients.
I hope your children will like one of them :)