Right now the tunnel to Whittier is closed to cars and it is uncertain when it will reopen. So you would need to park the car on the Anchorage side of the tunnel and take the train to Whittier in order to take the Prince William Sound tour, and I am not sure of the train times - you might need to spend the night in Whittier one way or the other. In any case, I think it would be a very poor use of your precious three days.
Train schedule's pretty abysmal. You either have 15 minutes to see Whittier or four hours. I'm not sure when the glacier cruises start doing revenue trips, but if the road's still not open by then, hopefully they rearrange the train schedules to meet better with those.
Train schedules here:
http://www.akrr.com/arrc115.html