I'll keep my recommendations to Tokyo:

I'd highly recommend the Fukagawa Edo Museum. It's a little indoor village, kids can go inside model houses and shops. When I visited I got an individual tour as it was not busy.
The Tokyo Railway Museum is great for kids, though it's a ways outside the city (but worth it).
Yokohama Ramen Museum also great if the kids like Ramen.
5 year olds love trains, so they will get their fill.

If you're looking for something high end that's also kid friendly, brunch at the Oak Door at the Grand Hyatt in Roppongi is a treat and is very ok for kids. For low-mid range, pretty much anything will be fine to take kids to.