Hi Sean,
I consider the northbound to be the best route. With the northbound or southbound routes, you'll get to see the College Fjord/Prince William Sound area, which is spectacular. Also, when sailing northbound, you don't have to get up at the crack of dawn on your disembarkation day to be on deck for the sail into Vancouver, which is really scenic. We also enjoyed our day in Seward, if that is available on some of the itineraries that you are looking at. Sailing out of Vancouver northbound is the best, in my opinion.
Happy traveling,
Donna