Having flown through Canada quite a number of times on floats & amphibs, the route that Skyhigh suggested would be the best. You do not want to jump from Whitehorse to Yakutat, that is very remote mountainous country with no where to land. And as stated before, stay away from the coast, unless you are going to install floats and don't mind flying really low.

The last plane(a 206 amphib) I flew up was from eastern Mass to Anc, it took 36 hours flight time. The Saratoga will, of course, make much better time. You'll get charged landing & ATC fees while traveling through Canada.

Have a good flight.