Just a quick caveat - if you want to go to the Studio Ghibli museum, be aware that you need to get tickets about 3 months in advance. There is a process involved.

Walking with them around the still active outer market at the Tsukiji market could be an experience for them and they could try lots of nibbles of different foods.

If they could handle a longer days activity, there are a number of bicycle tours you could look at. They'll often get you to areas of the city you would not tend to see otherwise