No, it is more like 2 hours 20 minutes from Tokyo Station to Kyoto. If you are going from Shinjuku, add 15 to 20 minutes for local trains to Tokyo or Shinagawa and take the shinkansen from there. Connecting at Shinagawa is easy. If you use Tokyo, add another 20 minutes.

As to the question of a JR Pass, the round trip Tokyo-Kyoto-Tokyo would make it pencil out but then you would be limited to Hikari shinkansens and add 20+ more minutes each way. At that time of year, I'd probably just spend the extra and not use a JR Pass so I could use the more frequent - and numerous - Nozomi trains. Hikari may be packed and difficult to get seats.

I agree with the above that a day trip from Tokyo to Kyoto is pretty much a wasted day as you will spend 6+ hours on trains and connections out of a short winter day. Kyoto is far better visited from Osaka as is Nara.