I've ridden all of those options that you listed and they all have points in their favor Here's a route that I setup for someone here who asked about Seatac to Anacortes: http://g.co/maps/hw2up
This more or less follows the Interurban to Everett and then a pretty direct route to Mukilteo. The routes on Whidbey and Anacortes are the most scenic routes - not the fastest or shortest. But the most off the highways and like I said the most scenic. This is pretty much the most direct route and you can camp at South Whidbey State Park or Deception Pass State Park if you want to split up the distance (its a bit less then 100 miles from your start point). Both of those campgrounds have hiker/biker sites.
Note that this ends right in Anacortes which if you want to go right to the ferry may not be what you want. However Anacortes is worth hitting for supplies, restaurants, pubs, the 24 Hour Donut shop &c. Then you just ride the signed 20 spur to the Ferry. However if you camped at say Deception Pass and wanted to ride straight to the ferry you should turn Left onto Marine Drive from Rosario Road and then Left again to stay on it. This becomes Anaco which takes you right to Sunset Ave where you turn right and you'll be at the road down to the ferry. I should say though that I really recommend my route through the center of Fidalgo as it's a nicer ride and beautiful.
If you go inland that is also great riding. You could do Edmonds to Port Townsend in a longish day. I'd camp at Fort Townsend State Park which is a few miles outside of PT and will cut down the mileage. It also has a great hiker/biker site. Don't skip out on Port Townsend Brewing
On the San Juan's themselves, well they are all great riding. Lopez is the flatest with only the climb up from the Ferry. Orcas is the most hilliest but very scenic, the most quirky and Moran State Park is excellent (Plus Mt. Constitution is must do). San Juan Island has the most riding and interesting historical things to see. Plus Friday Harbor is the biggest town out there and you'll find the most groceries, restaurants and pubs (though I hear the great Front Street Ale House is closed). Shaw is the smallest but not without its charms. It has a little county park there where the hiker/biker camping was super cheap and right on the beach. I don't recall there being much shopping options on Shaw (there probably is a general store but I can't remember it) so I'd bring at least some food supplies with you if you stay there. Orcas and Friday Harbor both have plenty of options.
The Vancouver Island option is a great choice - lots of great riding there plus Victoria is an excellent city. Good hostel there, plenty to see and do and a number of great pubs. I assume you'll ride the Lochside Trail from the ferry to the city, which is definitely the way to go. It rides pretty much right past the hostel once you get into the city (though its pretty much city riding at that point). It also connects right to the Galloping Goose Trail which is an amazing trail that goes pretty far up the western edge of the island. But whatever you do on Vancouver Island it will be nice. Looks like you are taking the Ferry back, the Victoria Clipper I assume. Note that with them you bicycle is more or less exposed to the elements and they recommend you strip off all your gear. So be prepared for that.