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.