Hi Larissa,
Yes the JR Pass covers all of this. Tokyo - Kyoto are about 160 minutes apart directly by Shinkansen, so it's pretty easy to travel between them. Tokyo - Sapporo takes a good time and will use up most of your day. Therefor I would recommend doing Tokyo - Sapporo in stages and making a stop on the way in between, such as at Sendai or Hakodate.
The 7 day JR Pass could certainly work for this and you can make very good savings over normal tickets. I would however advise looking at a 14 day JR Pass if you with to return to Tokyo/Osaka after Hokkaido as well.
Hope this helps,
Daniel