Howdy -

You can fly for about the same price as the bus/shuttle.
http://www.mgmbusservices.ca/
https://www.flyairnorth.com/servlet/...FlightsServlet
AirNorth had reasonable one-way fares to places in the Yukon and NWT.
Be aware that service is not daily and can change because of all sorts of reasons - especially weather.
Also be patient and don't have tight connections in your destination since they run on "Northern Time".

I connected with a bus from Whitehorse to Skagway and then took the Alaska Marine Highway.
The AMH also runs on "Northern Time" - but is certain to leave on time if YOU are running late.
The bus service was operated by Grey Line Tours - you might have to search the web.
CanadianNorth has jet service to Edmonton and connections to major Canadian airports.

Best - J