Hi Seth,
Let's start with Tokyo - Niseko, there's two options which you could consider. The first is going by domestic flight from Tokyo - Hokkaido (Shin Chitose Airport) and use a local train from there to Niseko. This is the quickest way but it is hard to say the price as ticket prices change by the day.
The other option would be to use the train entirely for travel from Tokyo - Niseko. This takes about 490 Minutes / ¥ 21,930. All trains in this route are included by the JR Pass and will get you back to Tokyo as well.
Note that you can also use the JR Pass from Furano - Nagano by train but it will also take 804 Minutes / ¥ 30,670. Which is a really long time, so I'd recommend looking into a flight here as well. Of course you'd be making great savings if you would use a JR Pass and travel by rail.
Traveling by night travel is pretty hard between Tokyo - Hokkaido, there are a couple of night trains but are almost always booked full well in advance and it is not something I would relay on.
I hope this helps!
Daniel
