My first question would be how much time to you have?
Port Hardy is unquestionably the best cold water diving I've ever done. But it's expensive, and you have to allow at least a full travel day each direction from Seattle. I'm going back up there in early March, and the cost (at The Hideaway, which is less expensive than God's Pocket) is $1150 for the week, excluding travel costs.
You can get in some outstanding diving elsewhere for a lot less money ... although it won't be quite as good.
Someone mentioend Campbell River/Quadra Island. This is diving in Discovery Passage, which is very current-intensive. The walls are amazing, although I don't think they're quite up to Port Hardy standards. There's a couple of all-inclusive dive operations on Quadra Island. If you don't have the time and money for Port Hardy, it's a very good alternative for some mind-blowing dives.
You asked about the San Juan Islands. Check into Friday Harbor. There's a local charter, easy access to some outstanding dive sites, and in winter both access and lodging at Friday Harbor is quite affordable. You can catch a ferry over there from Anacortes, which is about a 2-hour drive north of Seattle. Alternatively, you can dive some of the closer San Juan Island dive sites from Anacortes ... with either Lu Jac's Quest or Deep Sea Charters. Personally, I think the outer island sites offer more variety and the potential for better vis. The important thing to keep in mind is that the water's pretty cold in winter ... low 40's.
You asked about Nanaimo. It's also pretty accessible ... and the main attraction there is the wrecks, but there are some other nice sites available. Although there are some shore dive sites north of Nanaimo, most divers use the charters. Personally, I think Victoria offers more due to greater accessibility to shore dives (Ogden Point breakwater, 10-Mile Point, etc). You've got access to wrecks (McKenzie & Church), and Race Rocks ... which to my concern is one of the better dive sites on the southern side of the island.
I haven't been to Powell River, but south of there is Sechelt Inlet which has an all-inclusive dive operation called Porpoise Bay Charters that I really like. Winter diving is fantastic ... vis is usually in excess of 100 feet. There's also a wreck there (the Chaudierre) and some amazing walls and drift dives.
There's plenty of options ... to my concern, if you can deal with the cold then winter's the best time to dive here ...
... Bob (Grateful Diver)