A tad over three hours which I reckon should have been about enough as the check in time for the onward seaplane would normally only be ten minutes, Because of the Olympics we allowed one hour. Transfer between aircraft takes thirty minutes so would still have had in excess of one and a half hours in which to clear immigration and collect the bags. I wouldn't leave it tighter than that on our return we have a gap of three hours again but by then the Olympics will be long gone!
Have usually found YVR pretty quick to transfer through.