I have not participated to any cooking classes below but they may offer mochi cooking class:
* she has a Japanese sweets making course
ABC Cooking Studio
Maybe this is the most famous cooking class within Japanese locals. I did not know that they offer one-day course for travelers, but they seem to offer Japanese sweets (matcha tiramisu) making course.
During new year holidays, it is pretty common to do "mochi-tsuki". It's like an regional (communal) gathering in the new years and they take turns to make mochi. If you are lucky, you may be able to witness mochi-tsuki.
At Ichigaya Kameoka Hachimangu Shrine in Tokyo, they have annual mochi-tsuki festival on 23 Dec every year.
Mochitsuki Youtube video: