My 5-year-old daughter is a great traveler and she loves sushi.  I loved my previous trip to Japan, so I decided to take her there without my wife and younger, considerably less easy, son. Our goal was mainly to soak up the atmosphere and not aggressively sightsee, but we did always have a destination in mind to keep things interesting.  Here is a description of our experiences in Tokyo and Nikko.

Overall, we spent six days in Tokyo, with the middle three days in and around the small town of Nikko, about three hours by train to the north.  I wouldn't recommend this itinerary for a first-time visitor, but I'd been to other parts of Japan before.  There is plenty to do in and around Tokyo, and I wanted to minimize travel time.  Nonetheless, I perhaps should have looked for additional places to stay in the direction of Nikko.  While we had lots of fun in Tokyo, the many subway rides required to see the sights in this spread-out city got a bit old. 

Our Tokyo Hotel

One clear highlight was our tradtiional Japanese-style hotel or ryokan, Homeikan, which I found through Frommer's.  It was very friendly and authentic, and conveniently located in a pleasant residential neighborhood near the Kasuga train station.  The optional breakfast and dinner were superb and there is a beautiful garden that you can walk or sit in.  Those interested in soaking with kids in the large Japanese baths will appreciate their nice private family bath, as well as shared men's and women's baths.  There are several small restaurants near the station, and, most exciting for my daughter, there are about 15 beverage vending machines during the five-minute walk!  We also enjoyed several random walks in the neighborhood.  While I normally avoid the expensive Japanese taxis, we took several between Homeikan and the Ueno area when we had our bags, or when she got tired at night, since there is no good train route, and the fare averaged under 1000 yen (about US $8.31).

Favorite Tokyo Activities

We did the wholesale Tsukiji Fish Market the first morning and saw the cutting and selling of various fish.  While my daughter was intimidated by the frenzy (especially the motorized frenzy we walked through to get there), she still had some fun and I consider this experience an essential part of Japan for foodies.  Her highlight was shopping for snacks in the outer produce market.  Since we each had only one pair of shoes for the trip, I brought plastic bags and rubber bands to double-wrap each of our feet; this kept our shoes clean from the fish debris all around.

The toy store I chose to take her to was Hakuhinkan Toy Park.  While most of the items aren't especially Japanese, the place is enormous and we did buy polyester kimonos (also found for the same price at Narita Airport) and jigsaw puzzles with interesting Japanese scenes.  Lots of Hello Kitty stuff, too.  We also visited Bingoya, a lovely Japanese folk-craft shop, but they didn't have many toys of interest to a kid.

For another outing, we took the monorail, which leaves from right near Hakuhinkan, to Odaiba and rode the giant Ferris wheel.  It was fun and the views were nice.  There were a few other rides there – a dumb car ride and a free-fall ride that she was too small for, and, good snacks. 

Sanrio Puroland, the Hello Kitty theme park, was a mixed bag.  There was only one real ride (a tame but scenic indoor boat ride) and the shows we saw weren't interesting since we don't speak Japanese.  Nonetheless, there were many opportunities to interact with Kitty and friends, and while my daughter was a little disappointed while we were there, she was excited to go and speaks fondly of it now – and she's smiling broadly in all the pictures.  The cafeteria was atrocious; try to eat at one of the restaurants just outside. 

Seeking a more exciting amusement park but unwilling to confuse Japanese culture with Disneyland, we went to Toshimaen, the oldest amusement park in Tokyo.  Several new rides were quite good and since it was an off-season weekday, there was nothing close to a line.  The play structure, while a bit dilapidated, was great fun for her.  Unfortunately, the food was even worse than at Sanrio Puroland. 

She liked the Fukagawa Edo Museum more than I expected.  It's an authentic recreation of a 19th-century Japanese village and while it is small and indoors (unlike such exhibits in some countries), she still enjoyed it a lot. 

We had a great time in two large public gardens, one near Korakuen and the other near the Kiyosumi-Shirakawa train station (and the Fukagawa Edo Museum).  We wished we'd brought a nice picnic.  Ueno Park was fun, too.  We enjoyed watching and buying from the dozens of street food vendors at the south end of the lake. Great people-watching too. 

Tokyo's National Children's Castle sounded like a very promising attraction, but was a bit of a disappointment. The indoor pool is great but has only limited hours, which I don't recall finding on their website; you might call in advance if that's important.  However, there is a wonderful, large indoor play structure and there are lots of organized crafts projects that looked interesting, but she wasn't in the mood. 

Sidetrip to Nikko

A couple of comments on the train to and from Nikko:  While the private Tobu Nikko line from Tokyo's Asakusa Station is more convenient, if you have your choice of where in Tokyo to start from, the JR (or Japan Rail trains, without the expensive shinkansen or bullet train option) is more flexible since you can catch it from several places in Tokyo.  We started near Ueno and returned near the Shibuya Station, so it ended up being easier to take JR both ways.  Also, the regular JR trains don't require reservations, kids under six are free, and many travelers may already have a JR Rail pass.

We stayed at the Turtle Inn, which is well-documented in any guidebook.  It's very friendly and fairly modern, but not completely authentic.  The toilets were all Western (we liked the mix of floor-level holes and toilet seat ones at Homeikan), you can wear street shoes in the halls, and breakfasts are Western style.  On the other hand, we appreciated amenities like the clothes washer/dryer and Internet service.  The price is right, and I'd happily stay there again.

Nikko's main temple, the Toshogu Shrine was great, of course.  There was plenty to interest my daughter and there was a nice, extremely friendly restaurant just before the entrance.  But, the highlight of Nikko was a three-km. hike from the Turtle Inn to a rotenburo (outdoor hot spring) on the edge of town.  I don't know the name of the place, but it was quite elaborate.  They have very nice baths indoors and outdoors (I had no problem taking her into the men's baths), locker facilities, and an excellent restaurant.  Since it's out of the way, we sprung for a pricey taxi ride back. 

We also took a day trip to Lake Chuzenji-ko. The lake and waterfall were beautiful. We couldn't hike much at the top (in early April) because there was still too much snow; indeed, there was some snow in town.  But we enjoyed walking around town, shopping at a crafts shop and pedaling a duck-boat on the lake.  The highlight for my daughter was seeing monkeys playing in the fields and on the rooftops of buildings in town. 

That's most of what we did. I would be happy to answer questions about any of this for other families.