Coming to Tokyo in July with my family including 2 boys, 7 and 10 years old. We have the basic "tourist" things mapped out but we're there for an entire month. What are the little known places we have to take them?
Maybe museums? Like Miraikan in Odaiba (https://www.miraikan.jst.go.jp/en/), National Museum of Nature and Science in Ueno. (http://www.kahaku.go.jp/english/)
Ueno Zoo is also very big and enjoyable. There are two Giant Pandas may be rare to see in other countries.
There are also video game cafe/bars such as "8-bit cafe" in Shinjuku. You can play any video games in the cafe and menu are refers to icons in video games, such as name of cocktails.