The other three men -- Frankie Gonzales, Theron Parker and William Secor -- received two years of probation and between 100 and 150 hours of community service.
The Makah, who have been whalers for centuries, have sought to resume their hunts as part of their cultural heritage. The tribe have treaty rights to hunt whales, but must obtain a waiver under the Marine Mammal Protection Act before exercising that right.
The five men harpooned a whale four times and shot it at least 16 times on Sept. 8. The animal died nine hours after the attack. The men did not have a federal permit to kill the whale, which eventually sank and was not harvested.
After the hunt, the Makah Tribal Council called it "a blatant violation of our law." All five men admitted that they violated the Marine Mammal Protection Act.
U.S. Magistrate Judge Kelley Arnold determined that Johnson and Noel led the effort. Both men received longer sentences than the 60 days prosecutors had recommended.
As part of the sentencing, Arnold also said all five men have lost their privilege to hunt whales even if the tribe obtains a federal permit for a legal whale hunt.
Lawyer Jack Fiander, representing Noel, said, "It's not clear that the court can restrain them" from hunting. The sentence "was harsher than expected," he added.
Calls for comment Monday made by The Associated Press to the tribal council, and the tribe's Seattle lawyer John Arum, were not immediately returned.