Another vote for the Pan Pacific. We stayed there for 2 nights before our cruise in June. The first day, we walked down the pier to a bike rental shop and rented bikes to ride around Stanley Park which was really fun (and I do not enjoy riding bikes). Our room had a great view of the bay and Stanley Park. We also enjoyed watching the seaplanes takeoff and land.
The next morning was like Christmas when we woke up to see the Wonder just below our room (see picture below).
It wasn't cheap but nothing in Vancouver is during cruise season. I think it was worth every penny for the convenience. We didn't need a transfer the morning of the cruise from our hotel. Even better, we called the concierge desk and they picked up our bags from our room and delivered them directly to the ship so all we had were our carryon bags. It took longer to get through all of the security checks than it did to walk from our room to the port and it was nice not having to drag all of our big bags with us.
Keep watching because the prices fluctuate a lot so you might be able to find something fairly reasonable.
Jennifer