I'm not sure what your transportation situation will be like. The Pyramid brewery is in Seattle and is down on the Pike placemarket area. The market is a neat area with some interesting shops and of course the fish throwers that you often see on shows about Seattle.
The Pyramid should be reserved for a day when you walk the market area, then stop off at the Pyramid. The owner is very active in the microbrew community and has a sort of museum collection of beer memorabelia. That being said their beers are very standard fair for microbrews. They are designed to appeal to a broad swath of people who are in the area for the market. They don't make anything bad, but they also don't make anything that makes you go "wow"
The Elysian on the other hand has some absolutely wonderful things they do, from bold Porters and Stouts, to Jasmine IPA's, Wonderful Belgians, and often a Chimay if that is your thing. Go to the Pyramid for a nice experience, go to the Elysian for the real deal craft beers.
I have still not made it to Naked City, but have heard nothing but good things. Definitely worth a stop.They are at the top of my list of where to go, but I basically haven't gone out for a micro-brewed beer in a couple months.
Here is a yelp list of brewery type bars in the area.
Brewery Seattle | Yelp
Further north (about 20 miles) in Mulkiteo near the waterfront is a smaller place called the Diamond Knot. They make a double hopped industrial IPA. At about 8% ABV and enough hops to choke a horse, this one is serious if heavy IPA's are your thing.
Diamond Knot Brewery & Alehouse
There is a brewers festival about 10-15 miles northeast of the city in Kenmore if you will be here over fathers day weekend.
Washington Beer Commission - 2009 Washington Brewers Festival
The space needle is touristy of course, but is in a neat area with the experience music project if rock and roll interests you, and the Seattle center.
There are multiple small cruise ships that you can book for tours of the puget sound via the lake. They mostly leave from the waterfront area near the Pike market. They range from an hour up to a couple hours, and it's not a bad way to spend an hour or two and get a view of the the area from the water.