There is a bus shuttle called quickcoach.com that goes from Seattle to Vancouver. I haven't taken it myself but I've read good things about it. It leaves from a couple of different places.
We are taking the train. It's not the best schedule..it leaves at 7:40 in the morning or 6:50 at night. It's about a 4 hour ride but it's supposed to be along the water for a lot of it and a very nice trip.
Kelly