During my stay in Tokyo I had stayed at the Hotel Villa Fontaine Roppongi. It was a lovely hotel, not too flashy but clean and classy. Read my review of the same here - http://www.myyatradiary.com/2012/07/where-to-stay-in-tokyo-hotel-villa.html

The subway trains of Tokyo are a bit confusing at first but they are just awesome and connect the whole city like a web! Keep the map handy and you are ready to explore!

Places to Visit in Tokyo (links to my blog) - 

• Tokyo Tower (Tokyo Tower) - The kid will love seeing the city from high up in the sky!

• Epson Shinagawa Aqua Stadium (Epson Aquarium) - They always fascinate the kids, don't they?

• The numerous Gardens of Tokyo - I had visited the Hibiya Koen (Hibiya Gardens) and also the Tokyo Imperial Palace and their East Gardens.
• Take the Sumida River Cruise - Sumida River Cruises always provide a fresh perspective of the city!
• Temples - I visited the Sensoji Temple (Sensoji Temple) and the Meiji Jingu Shrine (Meiji Jingu Shrine). Both have beautiful architecture nestled among greenery and you will have a lovely time exploring them.
• Shopping - Nakamise Dori Shopping Arcade (Nakamise Dori Shopping Arcade, the road from Sensoji Temple leads to this one).

I was there for 3 days and covered these places. No doubt I would also have missed out on a lot since 3 days is not enough for a city like Tokyo!

I will also recommend you to visit the old towns of Nara and Kyoto. They have some ancient Temples and are not to be missed while in Japan.

Hope you have a wonderful journey to the land of the rising sun, if you have any follow up questions, I would be glad to help you :)

Odaiba has a lot of cool places for a boys or girls.