I live outside Seattle, and I frequently travel to Vancouver in my wheelchair. If you can afford it, the Pan Pacific is an excellent choice--you can easily get from the airport (YVR) to the hotel; they always have wheelchair cabs. The hotel is the cruise dock, so you are already there for your cruise. The hotel is beautiful--but expensive.
You will also have no trouble if you fly into Sea-Tac, just make arrangements first. The QuickShuttle (
http://www.quickcoach.com) has a wheelchair lift and will take you directly from the Sea-Tac airport to the Pan Pacific Hotel in Vancouver. You need to call to make sure they have a lift, but they are VERY reliable and my preferred method of transportation from the Seattle area to Vancouver. I don't like taking Amtrak in my wheelchair, for a lot of reasons.
Make sure you have all of the appropriate medical paperwork and information for the service dog. You don't want to have problems at the border.
Almost all public busses in Vancouver have lifts, and the city is very wheelchair-friendly. You may have trouble in Skagway, however, as the only accessible excursion is the White Pass Railway, and I would book it as soon as you can (don't wait for Disney):
http://www.wpyr.com/
They make a big deal about boarding at the dock, but the real truth is that the only difference is that you board from the front end of the train (the station) instead of the rear end of the train (the dock), and you have to check in at the station. It's the exact same train.
Make your reservations for the second train (in case you're delayed), but try to catch the first train out--we were told that we would have to split up the family, with one person riding with me. However, there's no charge for changing to the earlier train, and there were no wheelchair riders on the early train, so they put my whole family in with me, and we had the whole car to ourselves! It's a great excursion.
Have a wonderful cruise! I took last year's cruise, and I'll be taking the cruise this year from Seattle to Vancouver.