The train is operated by AMTRAK. It departs Seattle 7:45am from the station downtown, arriving in Vancouver at 11:40am. It is the most beautiful ride, right along the water's edge in many places. I recommend it. It returns from Vancouver in the evening.
The adult fare is $34.00 one way.
They have bus service as well between the two cities.
Check with AMTRAK for more info. Their website is very helpful. www.amtrak.com
We flew into Seattle and rented 2 cars (there were 6 of us and tons of luggage) and drove the beautiful 3 hour drive ourselves. It was a really easy route. You can drop off National cars about 4 short blocks from the dock. We could have walked it had we known how close it was. Full size cars were about $100. total each. It saved us about $250. pp on airfare. We went the day before the cruise.
We could not co-ordinate train or shuttle or anything else but cars with airline arrival times. They all leave Seattle too early to catch. Train goes too early in A.M.