Hi there!
You basically have two options traveling from Tokyo to Hokkaido.
The first is taking a domestic flight to Sapporo. This is faster than the train, however ticket prices can change by the day. Also all the procedures involved with flying will still take up most of your day.
The 2nd is taking traveling to Hokkaido by rail and here is here the JR Pass shines, just a one way Tokyo - Sapporo almost pays for a 7 day JR Pass. However do keep in mind that the full trip Tokyo - Sapporo takes 10 hours, even with the 320km/h Shinkansen and it is a good idea to plan a day stop in between.
These are basically the two best options, I've traveled from Tokyo (or even one from Fukuoka) to Hokkaido and very much enjoy taking the train, however in the end it comes down to your own preference.
Hope this helps!
Daniel