where in Japan will you be?
Parts of Tokyo would be fascinating for kids that age - the fish market is amazing, but a very early morning trip.
Away from Tokyo but not too far is the Izu Peninsula, that has amazing onsens (def something that you shouldn't miss) and also a gorgeous coastal drive.
Out of Tokyo Kyoto is a beautiful city, or Nara (you could combine the 2)
Anywhere in japan would be interesting - I lived there for a few years and would love love love to go back