We stayed at The Park Hotel, Shiodome. Great transport links and walkable to Ginza. It is modern and started on the 30th floor of a high rise. Not sure about family rooms though. Tokyo is a very business oriented city regarding hotels and they are not very family centred as far as we could see. Nor are there many boutique hotels. You may have to take two rooms and split the adults up!
There is a huge amount to see in Japan. I loved it! Tokyo is massive. It feels bigger than London. From Tokyo you can go out to Hase and Kamakura on a variety of railway trips which include the Enoden Line and a monorail. I bought a book on traveling using railways. I am not near my bookcase at the moment but I can find out the name if you wish.
The castle at Matsumoto is great and you can go up about 7 floors to the top.
The other great place is Kyoto and Nara. The fantastic temples in both locations are worth exploring. Tokyo has a great railway network and Kyoto has buses. It is easy to navigate. It is possible to see the Geikos and Maikos at about 5-5.30
Pm going to the tea houses in Kyoto. There are shops there that sell their hair decorations and kimonos. There are beautifully renovated tea houses and lots of dining options.
We also walked the Nagasendo Highway (check spelling) from Magome to Tsumago. Stay at a Ryokan. It is an experience and the Hotel Mume in Kyoto is superb.
The Lonely Planet guide is invaluable. It helps you decide what is important to you to visit because you cannot see everything. There are a couple of great gardens in Nara as well as temples and the park. Kyoto has Nijo Castle and The Golden Temple - there are plenty more to visit.
One other thing - July is hot! Pace your sightseeing. Food is interesting - plastic replicas of the dishes in the windows - you point. Or buy a fake geisha wig! So much is fascinating and the Japanese are very, very polite and want to please you. You can forward luggage the day before you travel onwards and it arrives at your hotel before you. You can then pack lightly for travel. Most stations have large left luggage areas. In big stations, these are vast areas and the stations are like towns. Remember where your locker is!
July is probably a good time to head to the "Alps" area of Sapporo but I haven't been.