Hi Erin!
I'm not too sure of your dates, but it sounds like you want to be travelling around Japan after Niseko for 2 weeks, followed by a week in Tokyo.
The good news is that the JR Pass is a nationwide pass, so will cover all your travel areas, including Hokkaido. The slightly less good news is that the journey time by rail down from Sapporo is quite long, coming in at 10hrs to Tokyo but you do see a lot of the country this way.
Assuming you travel down to Honshu by train, here are your equivalent JR ticket costs for comparison with the JR Pass prices:
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Niseko > Tokyo: ¥21,630 (603mins, 1057km)
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Tokyo > Nagano: ¥7,970 (105mins, 222km)
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Nagano > Kanazawa: ¥6,920 (241mins, 252km)
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Kanazawa > Kyoto: ¥6,910 (126mins, 224km)
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Kyoto > Hiroshima: ¥10,990 (112mins, 380km)
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Hiroshima > Osaka: ¥10,820 (109mins, 345km)
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Osaka > Tokyo: ¥13,950 (194mins, 556km)
JR ticket cost: ¥79,190 for 7 legs
As you can see, if you include the Niseko > Tokyo leg, you'll make great savings vs standard tickets on both 14 day and 21 day passes. If you flew down to Tokyo from Sapporo and started your trip there, you'll make great savings on a 14 day pass and break even on the 21 day pass while retaining the flexibility to change plans as needed.
I think your choice of 14 or 21 day pass here depends on 2 things:
- Will you take the train down from Niseko to Honshu or fly down?
- How much travel you think you'll do within/around Tokyo? The JR Pass can be used to get most of the way to Mt Fuji/Kawaguchiko (Otsuki station - ¥6000 return), Hakone (Odawara station - ¥7000 return), and used all of the way to World Heritage Site of Nikko (¥10000 return). It can also be used to get to Narita airport (¥3000) if that is where you are departing from. If you think you may visit these places near Tokyo, the 21 day pass may be a good option. The JR Pass can also be well used within Tokyo (here's a map of JR lines, although if you are staying 100% within the city and do not think you'll do the day trips I mention, I think I'd recommend you opt for the 14 day pass and buy subway tickets and so on as needed.
Knowing more about these 2 points will guide you in the following recommendations:
- If you fly down and will stay 100% in Tokyo for your last week, a 14 day pass is the good choice
- If you fly down and want to do day trips from Tokyo then a 21 day pass will be a good choice
- If you fly down, and want to keep Tokyo flexible, then you'll break even with a 21 day pass and retain flexibility.
- If you train down and will stay 100% in Tokyo for your last week, a 14 day pass is the good choice
- If you train down and want to do day trips from Tokyo then a 21 day pass will be a good choice
- If you train down, and want to keep Tokyo flexible, then you'll still save with a 21 day pass and retain flexibility.
These points are not exhaustive, but I think they should give you a good idea of which direction to go in.
Let me know if you need any more help, and congratulations!