Narita - Tokyo - Kyoto - Osaka - Hakuba - Tokyo - Narita

I am visiting in March 2017 to see my son in Hakuba but wish to make best use of my time from landing & departure at Narita to seeing Tokyo / Osaka and Kyoto aswell as my son.
What is the best route to follow to make best use of time and which pass if any should I purchase...I will be in Japan for 11 days in total
Thank you for your comments
Leslie