Just spent a week in Japan with my daughters...
who are somewhat older than your kids. The Harajuku recommendation is an excellent one, particularly on a Saturday or Sunday when the teen scene is really on. The neighborhood abuts the Meiji shrine which really makes for a contrast. Our kids loved the electronics district; the food halls under the department stores are fascinating for everybody and the Edo-Tokyo museum is a little out of the way but is a family oriented musuem with dioramas of life in Tokyo at different periods, well marked in English and with free English speaking tour gudes as well. Our absolute favorite thing was Tsujki the fish market, where did the real tourist thing and arrived for the fish auction, getting there at 6:15. Quite a show.
I agree with posters who question the one day trip idea to Kyoto. Recognizing that a diet of shrines for your kids might be a little much, I still think that, with the travel time, you need to allot two days, maybe including a side trip to Nara (75 minutes from Kyoto) where the mini-deer/temple combination is a lot of fun.