Accomodation with kids
You might find it's difficult to book accommodation for family in Tokyo .Although most of the hotels have room available for "2 Adults", when booking online, it is difficult to find a room for " 2 Adults + 2 (or more) Children, .
To circumvent this problem, when you find a hotel you like, contact the hotel directly by email or phone/fax and ask them if they can offer you extra beds for kids. Make sure you find a room large enough ( 30 square meters or more ).
Here are some kids friendly hotels in Tokyo.
Shibuya Tobu Hotel
http://ww2.tobuhotel.co.jp.e.fw.hp.transer.com/shibuya/stay/family/
Shiba Park Hotel
http://en.shibaparkhotel.com/room/
Keio Plaza Hotel
http://www.keioplaza.com/
Hotel Ryumeikan Tokyo
http://www.ryumeikan-tokyo.jp/english/