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.

Don't stay near Tokyo Disneyland. The area is the Japanese equivalent of strip mall hell, and while the Keiyo Line runs directly into Tokyo Station, you have to hike what seems like a mile through various passageways to reach any other train or subway lines.

Stay as close to central Tokyo as possible, and you'll be in Japan's transportation hub, whether you're talking about buses, subways, or surface trains. Taking the Keiyo Line on one day trip out of Tokyo wouldn't be too much of a strain. Using it as your first step in exploring Tokyo every single day would soon get pretty old.

Once you've landed at NRT, I recommend heading straight for the Tourist Information Center at Narita Airport and stocking up on all the maps and guidebooks they have. With a good subway/rail map, you'll be an old hand at navigating the transit systems in a couple of days.

By the way, to avoid having to stand in line at the ticket machines for the Tokyo subways and private (non-JR) surface trains, I recommend buying an SF Metro Card for each of you. You can recognize them because they're sold from ticket machines that say "SF" on them. You don't get any discounts from them, but you just insert them in the turnstile at both ends of the trip. They automatically deduct the correct fare for the distance, even if you transfer between lines.

There's a similar card for the Kyoto-Osaka area called "Surutto Kansai," but for your stay in Kyoto, you'd be better off buying one of the sightseeing passes that allows you to ride all the buses and subways in Kyoto for a given length of time.

I disagree with the poster who said that a week is long enough for Japan. I've been going there for 28 years on and off, and I still haven't seen everything. For a homogenous country, it has a surprising amount of regional variety.

Hear hear. Just yesterday I spent a whole day walking around the hills of Kamakura, and saw a fraction of the interesting stuff. Particularly entertaining was the Zeniarai Benten, since it was snake day, there was a boatload of people washing their money for good luck. I didn't even get to the singularly uninteresting "Great Buddha" of Kamakura, which everybody just has to visit on their half-day tour to Kamakura.

One could spend months in Japan and barely scratch the surface. It is one of the most complex and fascinating countries on earth.

To add on something, the SF METRO CARD is more widely known as the PASSNET card on most of the non JR rail companies in the Tokyo metro area.

Tokyo Metro calls it the SF Card and Toei calls it the T-card, however they are all compatable on the Passnet system. Its a good prepaid card if you're using non JR lines.

Right, the name for the whole system is Passnet, but I think it's easier to people who don't read Japanese to look for the "SF" on the machine.