Here are some random ideas:

The Sony place in Ginza has new high tech things on display to play with, IIRC on seven floors.

Kids might like tempura as it's basically french fried food. Yakatori is a great choice. There are also restaurants where you pick a combination of meat and veggies from a display case at the entrance and then grill it yourself at the table; I remember once going to one of these in the summer that was like an outdoor beer garden on top of one of the famous corporate headquarter buildings. There are also cook-it-yourself restaurants where the method is closer to stir fry.

Imperial Palace? Tour of Tokyo? The two big ferris wheels? The eco-dome (not sure what it's called--you see it along some bus routes from NRT)? Take the monorail to the Big Sight and take escalators to the top--this seems to be possible and free if it's open for an event? Nearby there seems to be some sort of family fun arcade.

I love to go into the food halls in department store basements to see the variety (things not eaten in the USA) and especially the shocking prices such as the hundred dollar melons with ribbon in satin lined wooden boxes or even the boxes of perfect fruit (including white strawberries) at gift times.

Some girls might like going to the jewelry floor of Wako department store in Ginza or window shopping in the watch stores (check the prices--I recall an emerald and diamond one for $400,000) of the Imperial Hotel Arcade. Check out all of the Frank Lloyd aspects of the main building. In fact, how about afternoon tea there in the lobby cafe or in a similar hotel? The lobby is great for people watching, and you're very likely to see some women in kimonos.

Be at one of the famous big department stores (such as Ginza branches) at opening time to observe the bows by staff.

Visit a Sumo stable or watch a match, even if just on TV.

If you have time for an excursion, Nara for the temples and charming little deer. [Apparently lime disease isn't a problem in Japan as everyone pets the friendly deer and feeds them. They walk up to you and will nuzzle pockets in search of food, but they're small enough not to be intimidating. IIRC there's even an underground passageway downtown near city hall that was built to help them cross a busy street.]

For a somewhat fancy lunch or dinner, consider the "floating" suspended restaurant in the art museum in Roppongi; the architecture of it and the building itself is interesting, IMO more than some of the exihibits.

I've never been, but there are a couple restaurants/cafes where you borrow a pet.

Sushi from the conveyer belt.

It's old technology now, but see a bullet train. Be in a subway station at rush hour when the pushers are working.

Around Christmas and New Year's, enjoy the holiday decorations in major department stores, buildings, and generally on the street in areas like Ginza.

Some kids might enjoy brief visit to a store that sells caligraphy.

As you walk around the city, pay attention to the traditional police boxes, including the one at the famous Ginza intersection.

The Japanese stock exchange has some displays, all labeled in English, to educate consumers in the Japanese approach to personal finance on a very basic level. Be prepared to laugh at some of the "facts." It's mostly electronic trading so there isn't much action on the stock market floor, but you can see the big ticker.

When you're exhausted from walking, take a river cruise through old Tokyo for an hour or two.