Best Pass for My Trip Plan

Hi,
I am going to go to Japan in April. Could you please suggest me the best pass or ticket for my below plan:

4-7 April: Tokyo
7-10 April: Kyoto
10-13 April: Tokyo.

So, should I get a JR Pass? I will only use train between Tokyo and Kyoto (2 ways).
Also maybe for Mount Koya and airport to hotel when I arrive to Tokyo. I want to use Shinkasen between Tokyo and Kyoto. I think JR Pass does not worth for my trip because it is in USD. Also I will buy Suica for metro in Tokyo and I heard that Kyoto is bus city.
What do you suggest? Also I m worried about that can I find available seat in the train because I cant book in advance here.

Thanks in advance

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