Originally Posted by mcg1000

If you are a family and are staying in Tokyo for more than a couple of days you may wish to consider one of the many serviced apartments (for example http://www.oakwoodtokyo.com/) in the city. They are much bigger than hotel rooms and relatively centrally located.

You could always try getting one of the larger rooms at The Claska (http://www.claska.com/) - for example a 46m2 room with a 56 m2 terrace is only Y52,500. The design is nice too (although the location is terrible).