There are flights from Vancouver to Port Hardy, and a bus from Victoria., Accommodation in both Port Hardy and Prince Rupert can be at a premium, which is why some people arrange this itinerary through a wholesale travel agent that specializes in Rail Tours, e.g. Fresh Tracks or John Steel.
After I read this suggestion, I looked unsuccessfully online for Fresh Tracks. I did find John Steel which has great options on their website but they don't answer their phone or respond to messages!
Just wanted to mention that Wendy from John Steel has been ill, now back at work. I can't fault her for not replying to my interest since she was in the hospital!