7 vs 14 day pass

Hello,
My husband and I will be traveling starting October 27th for 12 days...6 nights in Tokyo - 1 night in Hakone - 4 nights in Kyoto.

We are debating between booking semi private transfers for airport travel and the 7 day pass...activating it on the 30th or doing the 14 day pass (no transfers).
The price comes out to about the same so wondering which is more practical/comfortable.

I was also curious if the JR Pass covers travel to Hakone from Tokyo and then Hakone to Kyoto?

Thank you,
Maryn