Rail or Plane from Tokyo-Sapporo in Dec 2016?

I will be in Japan for 12 days to visit Tokyo and Hokkaido in December 2016.

Dec 23 – Arrive Tokyo overnight
Dec 24 – Tokyo to Sapporo
Dec 27 – Sapporo to Hakodate
Dec 29 – Hakodate to Tokyo (4 nights in Tokyo)
Jan 03 – Depart Tokyo

I am undecided whether to purchase the JR East South Hokkaido pass (Yen26,000) which will limit my stay to 6 days, or travel by air.

1. Does it make sense to travel by rail for 8 hrs to reach Sapporo? I have been told to factor in time involved when flying i.e. to consider travelling time/cost between hotel and airports including check-in time and the hassle of loading and unloading baggage. My Tokyo hotel is within the Tokyo Station area.
2. If I should travel by air, I can fly out immediately on Dec 23 to Sapporo since I arrive very early in Tokyo
3. Is 3 nights/Sapporo and 2 nights in Hakodate sufficient – since this is limit by the 6 day JR Pass.

Any advice much appreciated

the JR East South Hokkaido pass (Yen26,000) which will limit my stay to 6 days,

The validity is 14 days :
six days of your choice within a 14 day period.

http://www.japan-guide.com/e/e2361_southhokkaido.html