While you could go over to Bainbridge Island I wouldn't advise it. Likewise the San Juan's, you just won't have time.
For a nice hike with great scenery and good trails I highly recommend Discovery Park in Magnolia. The trails are well kept up and go right down to the water, and the lighthouse, and there's a nice place for sitting (or a picnic) at the Daybreak Star cultural center. This is right above the locks and you can often see (or hear) sea lions chasing salmon there. You can watch the boats too and see clear up to Canada if the weather's clear.
Anthony's Home Port is the local seafood chain, and fresh salmon and shellfish are definitely on the menu. If you go to Magnolia though, their lesser known place in the commercial terminal is Chinook's. Same menu, lower prices, fresher fish. This is where I get my salmon, basically right off the boat.
Check and see if the fish are running, because the other attraction over there is to go into the locks and watch the salmon run the ladders through the glass windows. This corner of Seattle is one of my favorite, and pretty much locals only.
The bohemian corner of the city is right next door; Fremont. If you're free on a weekend morning this is the place to check out, as they have a great open air market and the center of town is eclectic and designed for walking around.
In the city center, unless you really have need to be like every other tourist, stay away from the docks. If you are planning on visiting the Pike Place market try to go early, say NLT 8am, when they are still bringing in all the fresh stuff. All the commercial fish there comes from the terminal in Magnolia, so it's yesterdays catch.
Place's I'll recommend (in the city center) to eat are Wild Ginger, Flying Fish, or a little hole in the wall place called Kau Kau for Chinese BBQ (in the international district). (This is my go to when I hit the Pinball Museum for a couple hours fun on the games.)
In Astoria I like to eat at the Bridgewater, right at the south end of the 101 bridge, as much for the view as the food.
If you go down to Newport and visit the Yaqina Head lighthouse a good place to fuel up is the Rogue Ale Public House.
Further south, if you have the time, I like the Point Cabrillo Park as another good place to take a lunch and just find a quiet place to sit and watch the world go by. Good lighthouse here too.
Highway 128 from Albion to Geyserville is one of the great roads for a sports car that nobody knows about. It runs on an old logging road across the coast range into wine country. This was my Sunday drive when I lived in Napa.