flight from Matsumoto to Sapporo

How much does a flight from Matsumoto to Sapporo cost?

The flight operates on Mondays, Wednesday, Fridays and Sundays. The regular one way fare is around 33,000 yen, and there are almost no discounts offered, except the air passes for foreign visitors:
http://www.japan-guide.com/e/e2364.html

by almost no discounts offered, do you mean booking ahead won't make any difference?

Is there a cheaper way to get from Matsumoto to Niseko?

by almost no discounts offered, do you mean booking ahead won't make any difference?

Exactly.

Is there a cheaper way to get from Matsumoto to Niseko?

Take a bus to Tokyo and fly to Sapporo from Tokyo's Haneda Airport. On the Tokyo-Sapporo route you can get discount fares of around 10,000 yen outside the peak seasons:
http://www.japan-guide.com/e/e5306.html

thanks, Uji!

If time is not too tight, I have a feeling (but better check) that there is a ferry from Niigata (relaively near Matsumoto) to Otaru (near Sapporo).

But as I say: better check.

I am for slow travel myself.

there is a ferry from Niigata to Otaru but it is quite a long ride (something like 13-16 hours). See this page for more info:

http://www.japan-guide.com/e/e2355.html