Have you thought of Dineyland and the Disney Sea parks in Tokyo? Also Odayba is a great place to take your kids in Tokyo.
For Osaka, Universal city is a great visit, Den Den town is great for electronics gadgets and toys.
Also check out osaka-info this website has a lot of information listed for all kinds of things.
The peace museum is always my first recommendation, also if your kids love cars the Mazda museum is a good option.
Kyoto is mainly town for tradition and temples. Still most things are very impressive so this alone may keep your kids busy. For shopping I would recommend a walk trough Kawara Machi that boasts a wide range of small shops that sell everything. There are also video game arcades and local sweets available.
Hope this helps :)