Otherwise, try the Japanese version of Disney — Studio Ghibli. The Ghibli Museum in Tokyo showcases the work of the famed anime studio, but you'll need to buy tickets well in advance if you're keen to visit, as it can be booked up for months. Visit the official website (ghibli-museum.com). If your kids have never seen the movies, I'd recommend My Neighbour Totoro or Ponyo — it's a great way for them to get acquainted with Japanese culture before the trip.
Another fun activity for the whole family is going to a baseball game — even if you're not sports-mad, it's a great experience as the Japanese get really into it.
There are two teams in Tokyo — the Yomiuri Giants, who are akin to the New York Yankees, and the Yakult Swallows. They both play at the Tokyo Dome and Meiji-jingu Stadium. Tickets can be bought online or at Lawson convenience stores.
Kiddyland in Harajuku is one of the most epic toy stores I've ever been to and I can guarantee your children will love spending your money there. Capsule vending machines are also a fun way to pick up cheap little toys — Akihabara, the "electric district" of Tokyo is full of them. If you have any Hello Kitty fans with you, Sanrio Puroland will also be a hit — there are parades, rides and opportunities to meet and take photos with a number of characters.
The Ueno Zoo is worth visiting if they've never seen a panda before — I lost the plot at the sight of them and that was even before the baby panda joined the family.
The new Yayoi Kusama art museum in Tokyo recently topped Time Out's list of the 50 best experiences in the world and having visited her retrospective exhibition in Tokyo last year, I'd say kids would enjoy it too — her work is so fun and colourful.
Just outside Tokyo, Yokohama has plenty of kid-friendly activities — the Cup Noodle Museum is particularly unique, a tribute to the inventor of instant ramen. While you're there, you can design your own Cup Noodle tub and have it filled with the toppings of your choice.
There's also a great theme park called Cosmoworld, with an iconic Ferris wheel right on the Yokohama waterfront. And if anyone in the family is a petrolhead, the Nissan Global Headquarters Gallery will be well-received — it displays Nissan cars from past to present and you can sit in some of them.
If the adults are keen to visit temples, they need not be boring for the kids. In Kamakura, about an hour by train from Tokyo, the Big Buddha is sure to blow their minds. This surfy beach town with a Hawaiian vibe is a great place to explore on a day trip.
Back in Tokyo, the Gotokuji-ji temple in Setagaya is a treat for cat-lovers — it's where the lucky waving cat is believed to have originated and you'll see more than 1000 on display.
If you have picky eaters in your party, you should be able to find something they'll like at the numerous convenience stores — or if they're craving a Western style breakfast, Eggs 'n Things is the place to go. There are a few branches throughout Tokyo. Even going to McDonalds can be quite exciting — the menu has items you won't see anywhere else.
A sushi train restaurant is a must-do — the one I went to had a nifty system for returning used plates. You stick them into a slot and once you've returned enough, you might win a small prize.
I'm sure you'll all have a great time in Japan — I hope these suggestions are helpful.