Bellingham is a wonderful place, but has long wait lists. As was mentioned, Blaine, which has availability now, is run by the Port of Bellingham and so you do gain an advantage if you're waitlisted for Bham. We're in Blaine and have the following observations:
1. It's a beautiful, modern marina with a great staff.
2. Although it has no fuel, Semiahmoo does and is only just across the channel. Blaine tenants get a discount on the already excellent fuel prices in Semiahmoo.
3. There is a great yard with large vessel capability. They're easy to work with and can do anything.
4. It's 20 minutes from Bellingham by freeway, where all the other service facilities and marine supply places are.
5. International flights out of Vancouver are often less expensive than out of Seattle. We even fly out of YVR to New York on occasion due to the significant savings. It's easy to get in and out of YVR and inexpensive parking is available. It's the closest major airport to Blaine. Forget Bellingham...flights in and out of Bham are almost always much more expensive than either SEA or YVR.
6. Blaine is a few hours closer to the Canadian Gulf Islands and points north than Bellingham, La Conner or Anacortes. Yes, you do have to transit the Straits of Georgia, which can kick up at times. However, they're not particularly frightening to experienced boaters, no worse than some of the channels in the southern San Juans, and usually aren't a huge deal. The key is to consider both wind and tidal currents; when they oppose one another in some areas you don't want to be there in any size vessel. You're also close to the northern San Juans in Blaine.
7. The current exchange rate strongly favors Americans spending money in Canada. The greater Vancouver area (the "lower mainland") has many, many excellent marine repair options. Smart owners often take their boats into Canada for canvas work, engine work, etc. A friend just put a new diesel into his boat for about 30% less than he could have in Bellingham or Seattle; he had the work done in Nanaimo.
8. There are, indeed, many great opportunities for moorage in BC, both on the mainland and on the island. The previous poster was accurate in stating that foreign boats may not remain in BC year-round. I think that the current requirement is to leave BC after the boating season ends at the end of October. You can get a permit to overwinter in BC if you're having work done. Alternatively, you can pay the duty & tax and keep it up there year-round. Some owners keep their boats in the US during the winter, but move them up into BC for the summer season, flying back and forth to the US between cruises.
9. You will definitely need to pay tax either in Washington or BC; neither jurisdiction will allow you to remain long-term without paying state/provincial taxes.
10. For travel to Canada, you need a federal radio license from the FCC for your VHF, radar, epirb, and any other devices that radiate in the radio spectrum. Sure, lots of US boaters don't get this, but it's technically required.
11. You definitely do need a DTOPS decal from US CBP for returning from Canada. As was stated, a Nexus card greatly facilitates crossing the border, usually allowing telephone check-in rather than having to report to a designated customs reporting station; this only applies if everyone aboard is a Nexus card holder. A benefit of the Nexus is that it's a recognized "trusted traveler" program and can get you into the short line at airports. There's also a new phone app for returning to the US where you can do a video call to the officials for clearance.
12. Both Washington and British Columbia require a boater's card for boat operators. You can get one by taking an online course through BoatUS Foundation or can attend a physical class. BC grants reciprocity for Washington's card and vice-versa.
South Puget Sound has some lovely cruising grounds. The middle sound...Seattle-Everett...is basically an area to be transited rather than cruised. Port Townsend is a major center for boats and marine service, but requires you to transit the Straits of Juan de Fuca to get north (unless you go east around Whidbey Island and up the inside route). These straits can get pretty nautical at times; watch your weather windows and tides. The best moorage for quick access to the San Juans would be, in order, Anacortes, La Conner, Bellingham, and Blaine. Sidney, BC and surrounds are also close to the San Juans. The Canadian Gulf Islands and points north open up into a lifetime of cruising opportunities.