"They tried to climb back on the boat and it further capsized and that's when his mate was caught underneath it and drowned," said Ian Badham, from CareFlight, a rescue service.
"As he was trying to crawl to shore near the mangroves he had to use a spanner and sparkplugs, throwing things and banging at other crocs trying to get to him ... It was just a sheer act of desperation and survival."
The survivor was rescued by a group of fellow crabbers who helped to retrieve the dead man's body.
Authorities said the survivor was flown to Darwin and being treated in hospital.
"The man has been left suffering from severe shock and dehydration and exposure," Badham said.
The Northern Territory has about 100,000 crocodiles and has recorded numerous fatal attacks in recent years.
Authorities say there is increasing evidence that crocodiles have been attacking boats.