Sky tree and the Aquarium, its all in one building... The aquarium is really special its not to big or overwhelming, its all inside so a rainy day kinda thing or if its hot out, plus McDonalds is also located there, and a toy store with all kinda of gaming, like Mario, lots of different things and such.
Ueno Zoo and Park is another great option
My friends just got back from a almost 3 week trip to Japan. Their grandkiddo's the range from 3 to 8 or 9, her thoughts.
Nara deer park was a huge hit with kids and grownups alike
Universal Studios - . They spent 2 full days at Universal and the Osaka Aquarium both got high scores from them
On Odaiba - Legoland Discovery Center, Gundam Robot, Joypolis, along with Madame Tussaud's wax museum. She said that they bought some type of pass through Klook. She she they rode the trains, and visited over a couple of days. She did say there was alot of construction going on at ODaiba, and something where closed.
They also did a cooking tour, which she said was really fun, which everyone got to help prepare the meal. She said it was a highlight of the trip.
They also went on some type of Train tour, she called it the romantic train, and then came back on the river by boat. She said it was really beautiful. I'm really not sure on what this is called she kept calling it the romantic train. The photos are really beautiful.
They spent 5 nights( Hilton Tokyo Bay) and 4 full days at Tokyo
Disneyland. 2 days in each park.