Kitsune,
Yes, definitely Japan is good place to bring kids. I think they will enjoy themselves. Go Disneyland + DisneySea are already 2 full days well-spent. Then food wise is ok coz most places served kids' meals. If not, fast food is avail everywhere too. I think other sightseeing places are nice for kids to see and run about too. Like Hakone, Meiji Shrine, castle etc. Then there are also many indoor theme parks. I know there is 1 ice-cream theme park in Sunshine city.
Wah, your cousin lives there then can consider to bulk in. But keep in mind that apt in tokyo is very small so you got to check with your cousin if there is space for your family loh. Even if there is living room, the size is like our bedrm here. Then with the furniture etc, practically not much space to sleep.

Another thing is transport. Coz now there are still quite a lot of train stations that don't have lifts. So if bring stroller maybe a challenge. But they are building more now. Then dec quite cold. So got to buy winter clothes for your kids and then your luggage will be quite bulky.
Forgot to tell you that some factory outlets/shopping centres have play area for kids nearby so can keep the children occupied.
In short, JPN is a nice place. Hahahaha.
I also plan to bring my family there next yr.
But first, me should be going there in Aug.
Pixie,
Just book a flight and go there this weekend! Hahaha.