If you are going Mass market (royal carbbn., celebrity, Holland Amer, Carnival, etc.) look out to pick an itinerary with a "true" inside passage. Ships out of Seattle usually plow right into open sea. Ships out of Vancouver usually take the route closer inland (traversing the Seymour Narrows). Smoother ride and much more scenic. See this blog by a Holland Amer. Captain.
http://www.avidcruiser.com/albert/?p=441