Agreed with Richard that the Ghibli Museum might be the best bet, but it also might skew a little young for your kids. I wonder if they wouldn't enjoy a trip to the Akihabara district, or the Sony building in the Ginza, to check out all the electronic gadgets? Akihabara should have a decent amount of anime-related stuff, as well. Then there's also Shibuya and Harajuku and their, um, interesting, teen cultures.... especially if you can get to Harajuku on a day when the Gothic Lolitas are out.