Which JR Pass should I buy with 9D7N?

My itinernary:
8 Nov: Arrive at Narita Airport at 2025, Stay in Tokyo
9 Nov: Explore Tokyo, Stay in Tokyo
10 Nov: From Tokyo to Kyoto, Explore Kyoto, Stay at Kyoto
11 Nov: From Kyoto to Nara and Osaka, Explore both areas then back to Kyoto, Stay at Kyoto
12 Nov: Explore Kyoto, Stay in Kyoto
13 Nov:From Kyoto to Tokyo, Explore Tokyo, Stay in Tokyo
14 Nov: Explore Tokyo, Stay in Tokyo
15 Nov: Explore Tokyo, Stay in Tokyo
16 Nov: From Tokyo to Narita Airport, Morning Flight at 1040

Anyone please advise and explain on the best value rail passes to buy. Thank you very much.

A 7-day Japan Rail Pass costs about the same as a regular round trip ticket between Tokyo and Kyoto. Therefore, I would recommend to go for it.

But there are also a few cheaper options, such as overnight buses:
http://www.japan-guide.com/e/e2363.html

Thanks Uji. I have another query. Since my 1st day in Tokyo is late at night and my last day in Tokyo is early morning, should I exchange my 7 Day JR Pass only on my second day to fully utilise the pass? And does the 7 Day JR Pass include the Narita Express train to and fro Narita Airport and Tokyo city centre, Ikebukuro? if it is so, I would like to use it from 9 to 15 Nov. Can I stay overnight at the airport on 8 Nov and 15 Nov instead? Please advise. Thank you very much.

Yes, staying the first and last night at an airport hotel and using the 7-day Rail Pass from the 9th sounds like the perfect plan.

Yes, the Japan Rail Pass is valid on the Narita Express. Ikebukuro can be accessed by some direct Narita Express trains and is also valid on other JR trains serving Ikebukuro, including the most useful Yamanote Line:
http://www.japan-guide.com/e/e2017.html

Thanks Uji. I really appreciate it very much!