The creaky, funky, run-down marinas are usually cheaper. Crow's Nest on the north side of Commencement Bay is one that comes to mind. Nearby Tyee is probably reasonable too.
Stuff like 24 hour security
guards, nice bathrooms and laundry
, cement docs, shelter from the weather
, access to main channels, etc., all cost more.
Also, the further away from large population centers the cheaper it gets. You pay for convienience too.
Marinas.com might be a good place to start.