It's really up to the details... one possible option would be using a 7 day JR Pass along with a JR East South Hokkaido Rail Pass. The latter has a validity of 14 days and it's a flex pass, making it extremely versatile. However, the pass doesn't cover Asahikawa. It's unfortunate Japan doesn't have a lot more of these types of passes. With 14 days, it would be well worth it to stop at an interesting place along the way, such as Hakodate.
Along with Shirakawago, you'd need to take a bus to get all the way to Niseko.
The other alternative would be to get the JR Pass for going to Shirakawago and Kansai, and flying from Tokyo or Kansai to Sapporo. There are dirt cheap airfares on low cost carriers like Jet Star, Peach or Vanilla Air. Then perhaps a Hokkaido rail pass would work out for you.
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are excellent.
On another evening, you could also go and see Kobe.