Hi there,
If you plan on using the train between Tokyo and Sapporo (for Hokkaido) the JR-Pass becomes a really good option as one way costs ¥ 23,670 and the 7Day JR-Pass is ¥ 28,300 so if you made a return you could save at least ¥ 19,040.
A possible downside however is that the train trip to from Tokyo to Sapporo takes 539 minutes (or 9 hours minus one minute).
See Route 1 for reference. An option is to take the Shinkansen to Aomori and then take the night train Hamanasu from there to Sapporo. A normal seat is covered by the JR-Pass and you can save on accommodation costs.
How does this hold up to flying?
This is hard to say, flights are obviously faster and low ticket prices may be available but frankly it is hard how much it will costs until you start looking at ticket prices. The nice thing about the JR-Pass is that it is one amount and then you are all covered, making for easy budgeting.
The JR-Pass is really great if you plan on traveling longer distances in Japan but it is not very economic for just local travel, so if you are flying to Hokkaido you will be better of buying tickets locally.
Hope this helps,
Daniel