Honestly it is best to book the transfer with the cruise line. In the past there has been a program called US DIRECT in which the ship put your bags directly on a bus to the airport and you did not have to go through Canadian customs. Not sure if this is still in effect.
The bus gets to go through a special border crossing and can avoid up to a two hour wait at the border.
OTOH we had a great time renting a car in Vancouver and driving south, going on to the Chukanut Trail and stopping at an Oyster House for lunch. But AIRC we had a late flight when we did that.