When are you planning to go?
Also how long are you going to stay around Tokyo?
If you could stay around Tokyo for several days, I recommend you to take a short trip to near-by hot spring like Hakone area.
Hakone is quite nice hot spring area and kids can also enjoy. There are many places to see, too. I've been to Hakone area several times and I love it. I even took my in-laws (total 12 people including 3 little kids) several years ago.
You may want to stay Park Hyatt in Shinjuku and take Odaku-line to Hakone. It is not far at all. Just book a nice ryokan and stay a couple days. Actually, ryokan is a very nice place for family trip. They welcome kids, too. I've been staying ryokan so many times with my parents and grand parents since I was little. Don't stay at hotel type facility at hot spring. Many ryokan also have variety types of baths and you can book one just for your family for short time.