Hi! i am a licensed tour guide living in Nagano.
If you are coming from Tokyo, take Nagano Shinkansen Asama.It takes only about 100 minutes and no need to buy tickets if you have JR PASS.
At Nagano sta., take a bus to Togakushi Kogen (Togakushi Heighland) from the bus stop No. 7. This bus stop is a bit difficult to find; you need to cross a street from the Station Square out of Zenko-ji exit (not East exit).The bus ride will take 1 hour and the one-way fare is 1160 yen per person.
Get off the bus at Chusha-miya-mae and walk about 15 minutes.i usually go there by car, so i asked about how to get there by bus. I hope it is accurate.
It is a good place not only for kids but for grown-ups; you can rent a nija costume and try ninja-style athletic course in the park. There is a trick house like maze with many tricks and it would be the highlight. It is a mini size theme park!
If you are interested in ninja more, there is another place named Ninja Karakuri Yashiki (Ninja Trick House) a bit more geared to grown-ups or older children.
http://asobiba.jp/asobiba/contents/asobiba036_karakuri.htmI reccomend you stay overnight in a small traditional Shintoist Inn and enjoy their traditional meals including the village's speciality, Soba noodles.Even though Nagano city proper is famous for its delicious soba all over Japan, Nagano soba lovers go all the way up there just to eat their soba. Togakushi soba is a must.
I would also recommend you go up to the approach to Togakushi Shrine which is a unique Shinto shrine with mythological atmosphere; Togakushi used to be and still is a spiritual center for mountain ascetics and local people, as Zenko-ji temple in Nagano for Budhist monks, pilgrims and all the Japanese.
This is not a good HP, but you can get a feel for the place. If you like, see 'Togakushi Heights' in
http://w1.avis.ne.jp/~masuoha/Guide%20HP%20%20Nagano%20city%...Weather permitting, it would also nice to walk on the old trails for ascetics and pilgrims, taking a rest at beautifle ponds that reflects the magnificent Togakushi mountain range.
Before you go, please do not forget to check if those places are open; Chibikko Ninja Mura (village) is closed on Thursdays except for the summer and they and some of other places i mentioned will be closed in winter.
In winter, it snows a lot in this area ,so they have lovely ski slopes with ' real powder snow.'
Welcome to Nagano.
I really hope your family have enjoyable and memorable time up there!