The first consideration should be visa's. If you land in Seattle your three (or six?) month visa will start, and therefore expire earlier. If you then go up to Squampton, then you are burning up your US visa time. Trust me, three months ain't long to climb all the US has on offer.
If you fly into Vancouver then you get longer before you have to worry about visa issues.
You can travel between the two cities for anywhere from $40, if you do want to pop from one to another to purchase a car etc.
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