The attack took place near Gunn Point, northwest of Darwin, on Tuesday morning.
As the men were attempting to bring in crab pots a crocodile attacked, caused the boat to capsize and they were thrown into the water. They tried to climb back on to the boat, but it capsized again and a man was caught underneath it and drowned.
The surviving man was in the water for three hours. He threw tools and spark plugs at approaching crocodiles.
He was eventually rescued when other crabbers heard his shouts.
He was treated for severe shock and flown to Darwin.