Mmmm ... huge cites like these really aren't great for children. However, if you get out there are some fantastic day or overnight trips.
From Tokyo head past Yokohama to Kamakura, or try the Onsen on the Izu peninsula.
From Osaka head to Kyoto or Nara which are both more accessible to a 6 yr old.
We just returned from an amazing 3 week trip around Japan http://www.flickr.com/photos/simonmonk/sets/72157626899178429/with/5848789132/
How long are you planning to be there? about 7 years ago