Traveling with 4yo and infant

Upcoming trip, 2 adults, a 4 year old and an infant.
We are flying into Haneda and staying in Daiba, only plan the first few days is a reservation at TeamLab Planets and our plan is to adventure around Tokyo at a slow pace
Then traveling to Kyoto for 4 nights
Back to Tokyo, staying in Shinjuku, we have tickets to DisneySea
Then flying back out of Haneda

Is the JR Pass worth it? Do I need to purchase a pass for our 4 year old? I am seeing that the JRPass gets us a seat on the bus to Disney as well? All a bit overwhelming to decide with many different forums!