I would concur with the use of the cruise line transfer between Anchorage and Whittier. You may also consider taking the option of the train, if they offer it through the cruise line. As Cruise to Relax noted, the route would be the same, at least through the tunnel.
If you have a late flight leaving Vancouver after your arrival, there are shore excursions, perhaps through the cruise line and certainly with separate companies, that offer a day tour of Vancouver, with dropoff at the airport afterwards. Good way to spend the time (and have your luggage transported) - better than sitting in the airport all day!