We've cruised up and down the Inside Passage for the last three summers (Seattle to Haines or Sitka and back) typically returning in August—chasing sunshine—and then spending the winter in Friday Harbor. This season, we decided we liked SEAK so much that we moved to Alaska (PO Box, Driver's Licenses, Car, Boat Reg, etc) and are currently wintering in Petersburg. We also prefer to anchor, but in the winter it's pretty nice—and easy—to be on a dock near town, groceries, and other conveniences.
We absolutely love every part of BC along the way. While the scenery north of Cape Caution is hard to beat—and you could spend months exploring bays, fjords, and small villages—services get quite sparse between Port McNeill and Prince Rupert, with Shearwater being a notable exception.
Regarding NEXUS: if you're not transiting often, you can just use the designated entry ports on both sides. But if you’re going back and forth regularly, NEXUS will definitely simplify and streamline the process. Keep in mind that everyone onboard needs NEXUS to cross under the program.
We haven't had the opportunity to do the outside of Vancouver Island yet, but having gone outside of Baranof and Chichagof in the summer—when the Pacific is relatively calm—I wouldn’t be eager to be on the outside in the winter.
Many marinas have winter moorage rates, where they rent out long linear docks—used mainly for summer transient moorage—by the foot, and switch to reasonably priced monthly rates from about October 1 to April 1. Recently, I’ve seen ads from Deer Harbor, Victoria, and other desirable places along the IP.
And who knows—maybe you'll get the bug in a big way and end up here in Petersburg, Hoonah, or even Pelican. It’s pretty amazing up here in the winter. Rainy, yes, but quiet, lovely, and a lot of fun.