We just spent almost three weeks in Japan with our 6 year old (got back 19th April) and had an amazing time. We loved everything about it. We spent a few days in Tokyo then 3 nights at Tokyo Disney Resort. We then moved on to Kyoto, then Osaka (which we used as a base for visits to places like Hiroshima and Himeji) and finally returned to Tokyo for a few more days including a trip out to Hakone and Fuji.
We had 14 day JR passes and used bullet trains to get around, plus local train services obviously. We stayed in a mix of Western hotels, a Japanese style hostel (family friendly, with a private room) and Air bnb.
DisneySea is an amazing park, unlike any other Disney park and well worth a visit with kids. We also went to the Pokémon cafe, which was fairly newly opened,which was a great experience for our son (all the entertainment is in Japanese, but it was fun to watch anyway as the staff were all clearly loving what they were doing. Pikachu was so big he could barely squeeze pst the tables!) You currently need to book in advance and will need Google translate! We also went to the Ghibli museum which needs to be booked in advance - it has a Catbus play frame for kids under 12 which was fab.
As others have said, lots of free stuff too. Visiting markets (and sampling various foods) is a must do. The Metropolitan Govt Building in Tokyo gives great views. Wandering around Gion in Kyoto, the Fushimi Imari Shrine and climbing Mt Inari also in Kyoto. If you go to Osaka then Dotonbori at night is a must. I'd also recommend seeing Senseo-ji in Tokyo at night.
We were there in early April so saw cherry blossom but it was Japanese school holidays. Obviously their holidays are not related to Easter, so by going late April but before Golden Week you'll likely find it quieter.
I could write so much about our experiences but if you have any questions or want specific recommendations please ask!