I only see 2 major train legs in your itinerary, not 3; Tokyo to Kyoto/Osaka and back with a possible side trip to Kawaguchiko.
No sense in a JR Pass.

We enjoyed RiSuPia at the Panasonic Center in Odaiba when my daughter was around 5 years old. Language was less of an issue here compared to other museums, but that was nearly 10 years ago.

For History I’d recommend the Fukagawa Edo Museum which is satisfyingly hands on.

If your kid likes using her body to play, I HIGHLY recommend a day at Showa Kinen Koen. A bit of a journey to the suburbs to reach there, but it’s commuter distance “against the flow”. The tulips will be magnificent for your days and there are several large playgrounds with a wide range of equipment as well as a delightful Japanese garden and a wonderful bonsai collection. You can rent bicycles there too (the park is enormous). My daughter is 14 now but our yearly visits to Tokyo always included a day here (sometimes two) and, throughout every stage of her childhood, those days were always highlights amongst the many wonderful experiences we’ve had in Japan.

ETA
post #37 in this thread
Help plan family trip to Japan
was written fresh after a visit when my daughter was 4.5 years old