Originally Posted by
demue
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.
In that case it sounds like I should look at JR East Hokkaido rail pass, since it would take care of all the rail travel (Sapporo-Noboribetsu-Hakodate-Tokyo).