The key is to get there on a clear day when there is no rain. Check the weather beforehand and plan your trip. I've always had better luck shooting sunrise rather than sunset. There is also a very good chance of getting some nice alpenglow on the Olympic mountains. Sunrise in the winter is usually around 7.00 am. I would plan to get there about 15 mnts earlier and find some good spots.
One of the best places to shoot the ferries is from around the Ferry terminal in Seattle downtown. The best thing to do is to park around the Ferry terminal on Alaskan way and walk to the various piers around the area. One of my favorites is the pier next to the Argosy cruise counter.
Make sure to dress warmly as it gets pretty cold standing out on the pier for a couple of hours!