Hi Jerry,
You could either look at using a 14 day JR Pass + buy a one way ticket to Madarao (¥ 11,520) or a 21 day JR Pass (+¥ 12.960 compared to a 14 day JR Pass). The difference is minimal but you would have more flexibility with the 12 day JR Pass.
Narita to Madarao (Iiyama station) is about 203 minutes
Madarao - Niseko 505 Minutes
Niseko - no rail transport, you'd be looking at using an express bus or private transport.
Niseko - Tokyo is about 444 Minutes.
As you can see, going up and down to Hokkaido takes a good amount of time. You will be traveling on the fastest bullet trains but it still is a good distance to cover.
As alternative, you could look into air travel to/from Hokkaido.
Hope this helps,
Daniel