Hmm... cannot speak for using ponts in Tokyo- but I can say that the Mansions at Roppongi (in Roppongi) has larger suites for very reasonable prices which include a kitchen. The kitchen can save you a LOT of money AND grief as you can cook what your kids like. The caveat is the Roppongi area is very seedy at night- not at all in a dangerous way, but in a girls on the street kind of way. You can avoid this easily- no one will bother a family and there is little crime. The bonus is you are very close to subway/metro stations and can catch express trains all over the place. You also have enough space you won't go crazy, and you won't spend a fortune on a suite (which is not easy in Tokyo). The place is very family friendly, and (great bonus) very strict on not allowing any type of "shennanigans" related to aforementioned seediness to take place on the property.