Vancouver gives you much better scenery because you are literally on an "inside passage." That also means calmer seas.
We didn't get to Canada Place until 2:00 and we sailed right in. May have been crowded earlier.
First time we flew to Vancouver. Second trip we flew to Seattle and took Amtrak to Vancouver which was a lovely trip.
I would look for a cruise that does two out of three among Glacier Bay, College Fjord and Hubbard Glacier.