During our stay pre-cruise we only had one night in Vancouver before the cruise. We stayed at the Fairmont Waterfront Hotel right next to the cruise port. We found it a really convenient location because you can walk right over to the cruise terminal, there are places to eat/shop directly below the hotel, and it was within easy distance to several sight seeing options downtown.
We did book
DCL transportation from the airport, a bit pricey but it was our first cruise and we didn't want the hassle of figuring out transportation. On every other cruise since we've just used a taxi at the airport to get to the hotel, and again from the hotel to the cruise terminal if needed. It's not always the cheapest but we find it convenient. Most hotels will gladly pre-book a taxi for you, that can be really helpful in a small down (like Dover) where everyone needs a taxi to get onboard the ship at the same time.
A tale of caution on booking that return flight out of Vancouver. We again used Disney transportation to get form the ship to the airport, and we were quickly loaded on a bus once we retrieved our luggage. Our bus driver took us right to the airport, and then got lost. No seriously. We were on the first Alaska cruise for DCL that season and the bus driver was new. We drove all around the airport while he tried to figure out where to drop us off, we even sat in some far remote parking lot for about 20 minutes. Eventually he took us to the pick up point for passengers arriving at the airport. We probably added 30-45 extra minutes to our transportation time, all driving around the airport. At this point there was more then one family who was going to miss their flight on our bus. Once we arrived at the wrong spot, DCL staff went into action and helped guide us all and drag all our luggage up a small elevator to the correct floor for check in.
Thankfully we had booked a later flight, and while annoyed, were not super stressed. The downside was we couldn't even check our bags in until 3 hours before our flight, so we sat around in the pre-check in ticket desk lobby. There were a bunch of people from our cruise doing the same thing, so we all sat and enjoyed about an hour swapping stories.
Most of the time booking at flight after 11am is just fine post Alaska. You can be off the ship by 8:30am, and to the airport by 9:30 in a taxi. But sometimes everything doesn't work out ok. I'd always rather have a few hours to waste then a missed flight. I wouldn't book a flight that left before 1:00pm, just to make me feel conformation when issues like this arise.
Vancouver does offer a hotel onsite that allows for the 4 hour half day room option. We really considered this but just decided sitting in the airport was fine since we only had about 4 hours total to wait.
You can read about our experience at the Fairmont Waterfront here
http://frequentlyaskeddisneyblog.com/disney-cruise-alaska-part-17/
And our "free tour" of the Vancouver airport here
http://frequentlyaskeddisneyblog.com/disney-cruise-alaska-part-28/