Most areas in Tokyo have a Jidokan (child center) and are often attached to the ward office. Many of them have huge play areas with lots of toys. If it is a rainy day and you need a bit of a rest then these are a great option. There are lots of other kids there so they can entertain themselves for hours and if you feel like socializing with the other parents then you are more than welcome to.

If you are lucky, the library will also be in the vicinity so you can join and get some fun books out for your kids. Ring the English line at your local ward office and they will point you in the right direction.