Family trip

Hello,

My wife and I are traveling with two children (ages 3 and 6), and this is our travel plan:

March 6: Arriving in Tokyo around 3:30 PM, Narita Airport
March 7: Tokyo - City sightseeing
March 8: Tokyo - Nikko
March 9: Tokyo - City sightseeing
March 10: By car from Tokyo to Fuji
March 11: Fuji to Kyoto - Train
March 12: Kyoto - Arashiyama
March 13: Kyoto - Nara
March 14: Kyoto - Osaka
March 15: Kyoto - Evening train to Narita Airport

I am interested in the cheapest option. Should I buy a JR Pass (which one), or is it better to purchase individual train tickets? Which train lines should I use? Considering we are traveling with relatively small children, I would prefer to take routes with minimal transfers.

Thank you!