I live in Ballard too. I like BikeSport; they've treated me well in the last year and a half or so that I've doing business with them. Bought my first commuter bike (Giant Cypress) from them, and bought my sport-roadie (Giant OCR1) from them as well. They've generally been good about fixing small issues that crop up on the spot without charging me, and when I have had actual service done it's always seemed fast and well done. My gf's helmet is actually one of the ones on their rack of helmets that protected their riders in crashes.
2nd Ascent on Ballard Ave also has a good bike shop. It's not as complete as BikeSport, as it's only part of the store, but I bought my bike shoes and clipless pedals from them when I first upgraded the Cypress, and I've bought tons of non-biking stuff from 2nd Ascent. Further out there's a little bike shop in Fremont between NW 36th St and the Burke Gilman Trail that I can't remember the name of... then there's Speedy Reedy right on the Burke Gilman where it hits Stone Way.
Honestly though, my vote is to use your local shop. I can't even remember the number of times I've hopped on my bike, noticed some little thing wrong, and gone into BikeSport and had them just fix it right there. My guess would be that 2nd Ascent would be similar, as they did install my clipless pedals right there as I waited.