Just wanted to add to the Hayes River info bank.
As of May 2015:
To Fly out of York Factory on Gillam Air 204-652-2109 $1700 +GST no change from last year. No Otter from them but there is a Twin Otter on floats, in Thompson at around $5800
http://www.wingsoverkississing.comThere is a boat shuttle available.
Nelson River Adventures:
http://www.nelsonriveradventures.com/index.htmlWill shuttle you out for $3500.
Not sure how many boats he can fit in his boat but our quote was for 4 people two canoes. This is comparable to flying for larger groups.
This is a unique trip in that you get to go out onto the Bay and then up the Nelson to Gillam. Around 5 h trip.
Hugh