We've stayed at all 3 of those hotels right near the ships: The two Fairmonts (Waterfront, and Pacific Rim) and the Pan Pacific.

We much prefer the Fairmont Pacific Rim, especially if one can get a view of the water and across to the hills/mountains (not sure which category they are in!). Watching the float planes was fun, and in the winter, seeing the lights of the ski areas across the water was also fun. Tempting... but it's been decades since my skiing days (alas). Do try to get that view!
We did not car for the Pan Pacific at all, so we only stayed there once. Perhaps another stay would have been different.

We've stayed in the Gold level of both Fairmonts there. The Gold lounge in the Waterfront was more "clubby", which more comfy seating, less modern, etc. We tend to prefer that, but many others seem to prefer the more modern (and to us, less comfortable) furnishings. (This reminds me of comparisons between the F lounge for BA at Heathrow and the F lounge for Lufthansa at Frankfort.). Regardless, we do make good use of the Gold lounges at any Fairmont, especially the food.

At the Pacific Rim, they took us and our bags in a car, right to the lower level of the Pan Pacific to check our cruise luggage, even though it wasn't very far at all. Very easy; they handled all of the luggage and we just sort of trotted along. After getting our bags checked in, we went back to the Pacific Rim, to relax a bit more, and to get our few carry-ons before heading back to the terminal to board the ship.

Most of our stays in Vancouver were not for cruises, but for TED conferences after they were moved there from California, so the same location was useful.

GC