Hi,
Been thinking over the last day and here are some ideas, they may be out of date as it is sometime since we were there but at least it's a start for you to consider. Quite how you do it depends on whether your driving, how much you like driving, what exctly your family likes to do and how much time you have.
My holiday would comprise a start in Seattle, up to Mukilteo and ferry to Whidbey, up through Whidbey and to Anacortes, catch the ferry to Friday Harbor and/or other islands, ferry onwards to Victoria. Return via the ferry to Olympic Peninsular and Port Townsend and back down to Seattle via ferry and another day in Seattle.
In Seattle
The Klondike Gold Rush museum is interesting. Seattle was the last stop on the way to the gold in the Klondike, Alaska. The museum tells all about it and they have/had? a mock up of all the equipment each person had to take with them.
The Underground Tour was interesting. As far as I remember seattle used to get flooded with the tide, so they rebuilt at a higher level. This tour takes you around below the pavements to see the original streets and buildings.
Then obviously you have Pike Place Market, Aquarium, Pioneer Square, the zoo etc.
The Seattle Cente is home to space Needle, The Childrens Museum
A childrens Theatre and other entertainment although I think yours would be too young for EMP (Experience Music Project).
At Everett you may be lucky and pick up a home game for the Aquasox a minor league baseball team. Still professional but you're much nearer the game than at the Mariners and I think much more fun for the kids. Also Everett is a home to Boeing and if you are interested you can go on a tour of the factory (you need to be 4 foot tall though). It's near the ferry.
Whidbey and Anacortes
There is a [[http://www.swparks.org/parks_trails.html#playground
great playground]] outside of Langley. (You could catch a ferry as a foot passenger to Port Townsend from the west of the island.) Historic Coupeville is quaint. you have to cross Deception Pass bridge to leave the island but on the other side you can go to Bowmans bay and hire kayaks
San Juans
I am not so familiar with Friday Harbor as I only visited once but it has a great whale museum and is walkable from the ferry. You should be able to do some whale watching tours from here too.
You can catch another ferry direct to Sydney, Vancouver Is from Friday Harbor.
Another ferry company can take you onwrds and down from Victoria to the olympic peninsular. I never used this company but think you have to prebook.
In Port Townsend there is a fab fun fifty's diner complete with table top jukeboxes. Most of Port Towsned is walkable from the towns ferry dock, although Fort warden where they filmed An Officer and a Gentleman isn't really.
I will keep thinking of anything else you might like, but thank's for giving me the oppportunity to reminisce.