For the "young adults" - there are various manga and anime spots you can find by googling. E.g.,:

http://tsoj.manga.org/anime/anime_museums.html

Many will probably only have info in Japanese.

I've never been to any (not my cup of tea). We did go to Harajuku one weekend day on our second trip last year. Amusing - but probably more amusing for a teenager than us. And I don't really think a guide is necessary.

And I have couple of recommendations that might or might not be welcome. First - the idea of 2 adult males and 2 adult females sharing a single sleeping room with one bathroom is the antithesis of a vacation to me. Especially a perhaps once in a lifetime trip to Japan. Get 2 rooms. I assume there won't be a problem in terms of mixing sexes because your son and niece are cousins (and hopefully not kissing cousins).

I don't think it's your obligation to plan everything for your son and niece. Since they're adults who are presumably at least as good in terms of using the internet as you are - and Tokyo is perhaps the safest city in the world - and you're neither an expert in terms of the city or the language - ask them to plan what they'd like to see. Give them a budget - and buy them a subway pass - and then let them explore on their own. And you and your wife do what you'd like to do. You can perhaps do some things all together that you all want to do (maybe Disney - certainly some meals). But - there's no reason you have to do everything together. Robyn