To go via Anacortes is two ferries - one from Port Townsend across to Whidbey Island, then a second ferry that goes from Anacortes over to Sidney and I think that one makes a stop in Friday Harbour on the way. No contest. Going from Port Angeles is going to be much simpler. Don't forget your passports.
Perfect...and thank you for the reminder!
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FYI Feeding the seals at Fisherman's Wharf is not legal. I doubt that you will get a ticket but still not the best idea. Check out the You Tube video of the little girl getting pulled into the water by a sea lion. I believe that was at Steveston.
I always hit the Royal BC Museum. Check out IMAX which is attached to the museum, to see what's playing.
Also if you have never toured the Legislature Buildings, you might find it interesting. It's also free.