Tokyo w. kids

We're visiting Tokyo (7days) and Kyoto (2days) in April. Our family includes 3 kids of 9/9/5 years age.

We'd be grateful for tips about interesting sights for kids. These could also include some "must-see" or unique shops for kids ( toys etc. ) or restaurants. We're aware of Disneyland and Ueno zoo. Other than that we don't know much. Our youngest one is extremely interested in trains ( Shinkansen to Kyoto ), the older ones ( twins ) like technical things, Lego ( the boy ) and the girl likes animals.