I was thinking it might be better for you to fly directly to Victoria on Vancouver Island from Seattle. You could then stay a day and night seeing the sights in Victoria, B.C. and then take the ferry directly to the San Juan Islands. After a day and night in the San Juan Islands you could fly directly to SeaTac Airport in Seattle from Lopez Island, Orcas Island, or San Juan Island. Or you could take the ferry back to Anacortes and connect with a shuttle bus to SeaTac Airport.
Skipping the car rental and shuttle bus would save you valuable time. Avoiding traffic and the two-hour drive is another plus. The drive from Seattle to Anacortes is not considered a scenic route.
You will need a passport to cross the border. More details on travel documents can be found here:
http://www.dhs.gov/xtrvlsec/crossingborders/Without knowing more about what you are interested in it is difficult to recommend a particular island to visit. Orcas Island and San Juan Island have more to offer in terms of diversity of attractions than Lopez Island. I recommend you do a little bit more research on what each island has to offer you. Here are some good starting points:
San Juan Island Lopez Island Orcas Island How does this sound?