We just got back from Japan with our 8 year old son. In Tokyo, he enjoyed the Ninja restaurant, Ueno park and Odaiba (particularly the Gundam statue). He also liked the sword and drum museums, although the sword museum wasn't interactive and didn't have many english translations.

In Kyoto he enjoyed the samurai museum, the monkey park (Iwatayama) and Inari shrine. If you go to Osaka, there is a Kids play area called Kids's plaza that has a lot to keep them busy, particularly if it's rainy outside. There are multi levels of hands on exhibits and play areas.

Depending on how adventurous eaters yours kids are, they may enjoy the many small sushi, teppanyaki and ramen restaurants as well.

Have a great trip!