I'll only comment on the return to Tokyo, personally I would definitely take the Hayabusa to Tokyo as you are already in Hakodate. No point flying unless you are directly connecting to a flight out of HND or so.

Okay, Hakodate has plenty of nice onsen hotels / ryokans as well so you could do two days there and one in Noboribetsu, but depends what you are looking for. Noboribetsu is more for relaxing and soaking in the hot springs and not much else to do. Hakodate has a bit more to offer, but it is not Sapporo or so of course.