^

My own 9 year old is very active, an adventurous eater, and loves nature.

Her favourite places have been:

Fukagawa Edo Museum - I’d say hands down the best museum within Tokyo for kids to learn about local History. Combine with a visit to Kiyosumi Gardens. Right in front of the museum are a couple of restaurants specialising in Asari (tiny clam) cuisine - a very important food for the people described in the museum.

Day trip:
https://www.haneda-tokyo-access.com/...gro/index.html
Down to Misakiguchi for delicious tuna sushi and a trip in the mango “submarine” as well as exploring the rock pools of Jogashima (teeming with hermit crabs, fish and all kinds of life, the more you look, the more fascinating they become). Ticket price includes everything.
LapGirl chose to come for a second time this year - it was more her kind of thing than Enoshima.

Nihon Minka En
This is one of my very favourite places in Tokyo. Worth checking the website to see if any events are happening. Never crowded, even on the most popular days.

Showa Kinen Koen. My daughter’s very favourite place to visit. We come here at least twice on every trip. There are several playgrounds which are beyond wonderful. Also, a Japanese garden, beautiful bonsai, swimming pools and paddling opportunities in the summer (done the paddling in May but have successfully avoided Japan in summer swimming season - the pools do look good though!), cycling, boating, crafting, a lovely lakeside restaurant. This place has it all.

If your kids are young at heart - the Akebono Kodomo No Mori Park is small but unique. We honestly preferred it to the Ghibli Museum.
Note that you will need to bring your own food for picnics, it has no restaurant. Hard to explain why it is so special and satisfying for active and imaginative children - check it out with Google Images and know that the insides of the houses are treasure troves for hands on exploration.
It’s one of those places that won’t be nearly so special with much older (or with no) kids.

Tokyo Disney and Disney Sea.

My own kid’s “to do” list includes
The TeamLab Borderless exhibit already mentioned (we ran out of time and money on this occasion)

But, most of all, she is kicking herself for not having been aware of:

The TeamLab collaboration with the Haunted Horror House “showrunner” Mr Gomi at Tokyo Dome - the current one is called Onryou Zashiki.
I think you have to be 6 to be allowed in.

If we had the chance to go back this Spring for a vacation do-over, that’s what she would have found a way to fit in to the itinerary.

Her other favourite day trip was being in the snow (and the chair lift excursion was awesome) at Gala Yuzawa. We had JR East passes (went to see family in Matsushima/Sendai) but it can be done inexpensively with a Tokyo Wide Pass https://www.jreast.co.jp/e/tokyowidepass/
If you do go it’s one of the few places you can bathe together as a family. As well as the gender segregated sento, there are a non-segregated group of pools requiring bathing costumes and an outdoor jacuzzi with a view of the mountains.
Whether this is an option depends on the dates of your trip.
We live in London and spend time with family in Spain each year, so, on our Spring visits to Tokyo, this is the most economical way for us to experience snow