There's tons to do along the waterfront that appeal to kids like the aquarium and the Ye Olde Curiousity Shoppe.

Then take a ride on the water. You can take a real ferry. Maybe a trip to Bremerton (about an hour) and back again. Or shorter, scenic cruises on Puget Sound and/or Lake Union. You can also rent kayaks to explore Lake Union and its houseboats. If the fish are there, watching the salmon go up the fish ladders at the Hiram Chittenden fish locks is fun.

If you're getting a rental car, a trip to Mt. Rainier is only a few hours and can be tons of fun. Lots of great short hikes, including some interpretive hikes. And you can also go on ranger led hikes from the Henry Jackson Visitor Center at the Paradise location that are quite interesting. My kids enjoyed those. It's also fun to play in the snow on a hot day in your shorts!

I agree that the Museum of Flight is great. Kids love that place! However, I believe the Boeing Plant has a minimum age of 10 years old to go on the tour. I'm not sure if that's still valid so you might want to check into that. And, yes, kids love the Public Market with the "flying fish".

I can't imagine any kid not loving going up to the top of the Space Needle. There are a few rides and a midway at Seattle Center where it's fun for the kids to blow off some steam and sometimes they have events there that are geared to kids.

And Bill Speidel's Underground Tour of Seattle is a kick even for kids. They get to walk around "underground" in the old abandoned areas of Seattle and it's kinda spooky in a fun way. My kids loved it.

If I think of something else, I'll pop back in here.