Two of the teens, aged 15 and 17, who can't be named under the Youth Criminal Justice Act, each received 200 hours of community service and were fined $1,000 during their appearance Thursday in Georgetown provincial court.
Colton Hal Clements, 18, was sentenced to probation for two years and was fined $1,500.
The three had pleaded guilty to animal cruelty stemming from the incident at Beach Point, near Murray Harbour, on Jan. 26.
The probation and fines set are the maximum for young offenders. The maximum sentence for adults for animal cruelty is five years, but that is not available to youth.
Custody for youth is a last resort and rehabilitation must be emphasized, Judge Nancy Orr said.
"While the circumstances are serious, personal circumstances of the two youth indicate jail is not appropriate," said Orr.
She said the boys are considered by all interviewed for the case to be "decent teens."
Seals didn't die quickly
"They did not expect the immediate and severe reaction to their behaviour," said Orr. "They now understand what a big deal it is. These youth are not anonymous in their communities. They have experienced first hand the shock and outrage of their community.
"The harm you did cannot be undone. You will need to work to regain the trust of your community. You both have strong family support and must rely on that to correct your mistakes."
The court heard that the 15-year-old, who was with Clements, came up with idea to club seals. They called up the 17-year-old and drove to the beach, where they could hear the cubs barking.
The boys used a club, hockey stick and a metal tool for harvesting clams, known as a clam hack, to bludgeon the seals.
The 15-year-old killed most of the seals with the clam hack. The other two boys killed a total of seven or eight animals.
The boys threw the weapons away. One of them burned the hockey stick the next day.
According to an agreed statement of facts read out last Thursday in court, 49 of the 65 seals that were found bloodied, dead or dying were seal pups.
A necropsy showed blood was found in the seals' lungs, stomachs and wind pipes, indicating some of the animals did not die quickly.
'Unresolved' anger issues
According to the pre-sentence report on the 15-year-old, the Crown said he may have "unresolved issues with anger in his life" related to family problems.
The presentence report said that, while growing up in fishing community that regards seals as harmful may have influenced the boy, he "knew right from wrong."
"Seals are like mice running through cupboards," he said. "I hear it all the time and I thought I was doing fishermen a favour. I just did it with no thoughts about the animals. We are hunters. It was wrong and I am sorry the animals suffered.
"Even when I was doing it I thought it was wrong. I had a funny feeling in my stomach, but I kept doing it. I wish I could take it back, but I know I can't. I did it myself and will just take the consequences."
The boy, who is described as quiet and respectful, has written a letter of apology to the federal Department of Fisheries and Oceans. He said he is willing to go to counselling.
Police found an unsecured shotgun and three shotgun shells in the 15-year-old's bedroom when they executed a search warrant.
He was charged with unsafe storage of a firearm and pleaded guilty.
Last week, Orr handed him a two-year weapons prohibition, starting immediately.
The court also heard last Thursday that the 17-year-old was drinking the night of the attacks. The other two were not.
Clements's lawyer, Jonathon Coady, read to the court a letter from a Murray Harbour fisherman that said in part, "Most of us local fishermen are partly to blame. We never say anything good about seals."