You will probably want to visit orcas Island or San Juan Island as they have the most to offer as they are the most commercialized.  If you are seeking less commercialization you might try Lopez Island or for extreme non-commercialism you can check out Shaw Island.

The ferry ride is about an hour to an hour and a half depending on which island and weather.  Orcas Island features Mount Constitution which is about an hour drive from the ferry landing and takes you through Moran State Park which is a beautiful drive.  San Juan Island has Friday Harbor, Roche Harbor, where you will find restaurants, galleries, and shopping.  I'm sure you will be happy with either island.  Orcas Island definitely is more spread out which would mean more driving however the drives are very scenic and the destinations are unforgettable.

A recommended drive on San Juan Island:
get off the ferry and park for a quick walk around town and bite to eat.
Stop at the grocery store to pick up some driving snacks.  The grocery store is right in town.
Get back in the car and start heading out cattle point Road. 
Make sure to print out a map of the island.
Visit south beach, and the cattle point lighthouse.  Both destinations have good parking and feature photographic opportunities.
Get back in the car and take cattle point Road back towards town and take a left on false Bay Drive.
Then take a left on Bailer Hill Road and continue straight up and down the Bailer Hill.
At the bottom of the hill take a right onto Wold Road.  Continue for about one half a mile until you see the lavender farms on your right hand side.  The lavender farm has a small gift shop, a spa, some sculptures, and a massage spa.

Continue your journey by going back the way you came from on Wold Road until you get to Bailer Hill Road.  Take a right on Bailer Hill Road which shortly turns into West side road.

West Side Road is a spectacular drive that takes you by the following: dead man's cove, Limekiln State Park/whale watch park, and San Juan County Park.  Limekiln State Park is a bit of a walk from the parking lot.

Continue on Westside Road and take a right onto Mitchell Bay Road.
Take a left onto West Valley Road.  British camp will be on your left and is also a short walk from the parking lot down to the gardens and structures.

Continue on West Valley Road and take a left onto Roche Harbor Road which will take you to Roche Harbor Village.  When you see the Roche Harbor archway vear to your left passing the Wescott Bay sculpture park on your left and then stick to the right until you reach Roche Harbor Village.  At Roche Harbor you will find a small grocery store, a historic hotel, a full-size marina, a couple restaurants, a wedding chapel and gardens.

You can visit the Wescott Bay sculpture Park before or after visiting Roche Harbor Village. 

Take Roche harbor road east all the way back to Friday Harbor which is about 10 miles.  Spend whatever remaining time you have exploring the shopping, restaurants, music shops, antique shops, galleries, toy stores, and Whale Museum.

Parking your car in the ferry line before exploring might work depending on the ferry times and how much you want to see.  Otherwise move your car back into the ferry lines about one hour before the scheduled sailing ferry departure.  During the summer months you will want to get your car in line several hours beforehand.


That is my suggested San Juan Island daytrip routine.  Enjoy!