I'd stay in one room in one of the luxury hotels. Some of the Tokyo hotels are really fantastic, and have quite large rooms.

I've stayed in the Grand Hyatt with a family, which has a decent-sized room with two decent sized beds that I know holds 4. I think it's called a Grand Deluxe. If you have Hyatt points, you can use 6000 to upgrade to a fantastic suite for four nights. This room+points is one of the best values I've seen anywhere!

Four Seasons I know can hold 4/room in either a deluxe or premier (can't remember which).

I thought Park Hyatt capped out at 3 now, but possible that if kids are young enough, they will allow 4.

I know Pen only allows 3 max, and I think the same is true of the Shangri-La and MO.

Personally, I would go for either FS (fantastic location, boutique hotel) or Grand Hyatt (also great location, great hotel and if you can upgrade w/ points is a pretty unbeatable value).