Don't know if this is a possibility for you, but Air Canada flies to Vancouver from Anchorage over the summer. Award availability can't be too great though.

Personally, I would go for the later flight. Seattle airport is easy to get around, and you should easily be able to make a connection, even after claiming your bags, of 2hrs. But, I would be worried if the inbound flight is late for any reason. I would want more time because of the separate reservation.