Directions to Canada Place cruise port from Via Rail Station (which will be your arriving station if coming by Amtrak):

Walk to the Main Street - Science World Station (skyline) by going South on Main Street. Take the Skytrain to the Waterfront station. Exit the train to your left and you will find your way to the cruise ship.

Price: $2.50
Time required: About 15min.

Directions to Canada Place cruise port from Vancouver Airport:

Take Canada Line train to Waterfront, then walk to cruise port. The Canada Line Skytrain Service is a light rail service from the airport to downtown. It takes around 20 minutes to get downtown. Get off at Waterfront Station for Canada Place.

Price: $7.50
$5 (YVR AddFare for trips including the airport) + $2.50 (regular fare) = $7.50. More info at Translink.

Time required: About 35min. (includes waiting & walking time)

Directions to Ballantyne Pier cruise port from Via Rail Station (which will be your arriving station if coming by Amtrak):

Ballantyne Pier is a short taxi ride from Via Rail Station. The taxi fare from a downtown hotel or the Via Rail Station is about $20.00 to Ballantyne Pier including tip.

Price:

Taxi: 20 dollars

Time required:

Taxi: 10 minutes (excluding wait to find a taxi)

Transportation from Seattle to Vancouver:

DON'T OVERLOOK CRUISES: From time to time, cruise lines offer 1 day cruises between Vancouver and Seattle. If you're in luck, you may find one which fits your schedule. Since these 1 day cruises are "repositioning" cruises, they tend to be cheaper.

By Amtrak train: The train between Seattle and Vancouver makes a very scenic run, and avoids long waits at the border. You will find that a regular train seat is about as comfortable as an airplane business seat ; you will also be able to walk freely within the train (by enjoying the dining car for instance). Train Cascades #510 leaves Seattle at 7:40 AM (arriving in Vancouver at 11:40 AM) ; while Train Cascades #516 leaves Seattle at 6:50 PM (arriving in Vancouver at 10:50 PM).

Quick Shuttle offers bus service between Seattle Tacoma Airport, Downtown Seattle, Bellingham Airport and Vancouver. While Amtrak would probably be more enjoyable, Quick Shuttle does provide bus transfers directly from the Seattle Airport to Vancouver's Canada Place cruise port.

Luggage Storage at Canada Place:

Priority Baggage operates a luggage storage facility at Canada Place Cruise Ship Terminal. You can leave your luggage at Canada Place after you get off your cruise or before you board. You can even have your luggage transferred to the airport so you can spend the day exploring Vancouver without having to lug luggage.

Carry-ons are C$5.50, suitcases are C$6.50 and oversize items are C$8.00 a day. Luggage storage is available from 5:00 AM-1:00 AM. Call 604-303-4500 for more information.

External resources:

Skytrain (Expo line links Via Rail to Waterfront)
Canada Line Map(Airport line)