I’d love to ride it one way, and then the Alaska Ferry down to Bellingham.
Some bad news for you: that is not, and never was, possible, unless you want to also spend a few days in Alaska. The Alaska Marine Highway runs from both Bellingham and Prince Rupert to southeast Alaska, but not from Prince Rupert to Bellingham. Ships go nonstop from Bellingham to Ketchikan.
In a year with neither a pandemic nor an Alaska state budget crisis there will be 2 sailings a week to Prince Rupert and to Bellingham. In 2020, with both, there is one sailing every two weeks to Bellingham, and none to Prince Rupert.
A Canadian ferry from Prince Rupert to Port Hardy, BC, is also an option. In a previous era it would have been met by a bus that would have taken you to ride the Malahat.
Random VIA trivia: the ferry terminal is just south of downtown Prince Rupert and you have to cross the tracks to get to the dock. I saw my first Skeena go past while waiting in the queue to board the ferry to Alaska, one morning in August of 1993 (the Skeena was on the overnight schedule then and got into Prince Rupert about 10 in the morning. It was close to on time.) One F40 and four cars.