What would be the best option for our family 2 adults and two children ages 11 and 6 years old

We will be arriving at Narita airport Terminal 1 on December 12th at 3 in the afternoon and will need to travel to Shinjuku to our hotel in Tokyo. We will stay in Tokyo for 4 days and then travel to Kyoto on the 16th. We will then need to travel from Kyoto back to Tokyo and then to Narita airport Terminal 1 on the 19th for a flight home at 6 pm. We plan to take the Shinkansen in first class whenever possible. What are the best options for us? Should we get individual tickets or the JR pass for all of this? Does the JR pass allow us to get from the airport to Shinjuku? Thank you in advance for your help.
Sincerely,
Frank