The incident involved a rescue in the waters off Port Hardy Sunday night.
The crewmembers had called for help, saying the skipper was high on drugs and threatening to kill them.
The skipper was arrested after the crew jumped to safety aboard a police boat.
Karl Darwin Thomas, 49, of Courtenay, has been charged with assault with a knife, uttering threats, pointing a firearm and careless use of a firearm.
He is scheduled to appear in Port Hardy Provincial Court on Tuesday.