I've been to only a few smoke shops.

Those two seemed to have pretty good pieces by my standards and Holy Smoke has got some awesome water pipes and other little goodies. There was one more on Capitol Hill but I can't think of the name. If you happened to know of Laughing Budda Tattoo, it's located right under that.

Holy Smoke
Located on John right off of Broadway. A few buses that stop near there, 49, 8, 43
1556 E Olive Way, Seattle, WA

Last Stop Smoke Shop
Located right off of 55th NE
Not quite sure about the buses though
4539 University Way Ne, Seattle, WA