There is a place called "KidZania" in Tokyo and Hyougo which is near Osaka. KidZania is a Theme Park where all kids can experience and learn more than 90 jobs in uniforms!! Limited numbers of avtivities are conducted in English too. http://www.kidzania.jp/tokyo/en/
When you want to eat some Japanese foods with your kids, "family restaurant" could be an options. There are many these franchise restaurants ( Denny's, Saizeria, jonathans..). Usually, they have a spacious tables and many kids menu. Prices are really reasonable too!