Prince Rupert has some frontage where the RCN could build a dock. However the land is only a couple of hundred metres wide, has a active rail line through it and is heavily contaminated. CN will be happy to sell/lease at heavy price no doubt.
There was a ammunition resupply site at Port Edwards/Watson Island in WWII, now a propane terminal. The entrance is narrow but deep enough. The best place is on the same island as the airport, there be enough room for a couple of ships, small support base and some ammunition bunkers.
All bunkering at PR is done either from barge or truck. There is one small fuel station for smaller vessels.