I took Amtrak from Vancouver, BC to Bellingham in May. Without a doubt, Amtrak would be the cheapest and most comfortable way to get to Seattle.
Yes, there could be an interruption from a problem with the tracks, but Amtrak provides alternative bus service in the case of train interruptions.
You do not need to book in advance, and you can ask Amtrak if there are any service interruptions on the day of your travel.

In Vancouver, the passenger train station is accross a street from the nearest elevated transit stop. You clear U.S. customs and immigration in Vancouver, so allow a little time for that.