It's been a couple years since I lived up there, but here's what I remember (in order of personal preference):
The best is this place: http://www.americaneagleshobbies.com/ They've got a big store on the northeastern end of the city; I only went there once, but was thoroughly impressed. They also have a smaller store in Tacoma which has more of the LHS feel (packed with models anywhere they fit).
There is a Hobbytown USA in the Southcenter mall area (Tukwila)... it's across the street from the Azteca restaurant.
The Museum of Flight gift shop has a decent selection of kits (almost all airplanes... no surprise), and the exhibits are pretty cool, too.
Skyway Model Shop (http://www.skywaymodel.com/) is sort of on the border of Renton/Skyway. They had a slightly more diverse selection and more aftermarket stuff than Hobbytown, but they were a bit out of the way for where I lived.
There's a hobby store on Main Street in downtown Auburn; don't remember the name (Wagners Ultimate Hobbies?). For how big it was, it had a very small selection of aircraft kits; slightly more armor. The shop was mostly RC and model rocketry.
I don't know how much time you're planning to spend in the area, but happy hunting.