Cabs? That's how to do things the most expensive way possible and miss much of the point of visiting Japan. Yes, cabs are great when you are moving luggage or have stayed out past the trains, but if you're sightseeing, you're going to want to move around the city, and those (more like) $15-20 trips add up.

On trains and subways, children under 12 travel for a lower price, so with three of you on the subway or train, the price will be closer to $6-8 per trip. Get a Suica card (they come in adults' and children's versions), and you can pay your train and subway fare simply by touching your card to the sensor on the turnstile. If your Suica card runs out of money, you can add value to it at any train or subway station.

The train/subway system can SEEM intimidating. When I first went to Japan many, many years ago, I stayed in the YWCA until my apartment was ready, and there were some women from Australia who had come to attend an international convention. They had not been out sightseeing, because they were intimidated by the train system, so I took them on my next scheduled outing. I think we went to Ueno Park and Ginza. At the end of the day, they said that they regretted not venturing out before, because the train system was really less confusing than they had thought.

There is nothing like Tokyo's transit system in the U.S., and I consider it an essential part of the Tokyo experience.