U.S. District Judge Valerie E. Caproni noted that the sentencing of Joseph Percoco occurred amid other recent high-profile convictions of state leaders.
She said those seeking the modest salaries of government jobs should not seek to supplement their incomes by accepting bribes.
"If you do so, this court will show you no mercy," Caproni said.
Percoco, 49, was convicted in March of accepting more than $300,000 from companies that wanted to gain influence with the Cuomo administration.
The judge drew a parallel to her recent sentencing of Democrat Sheldon Silver, the 74-year-old ex-New York Assembly speaker, who begins serving a seven-year sentence next month after his conviction in a $4 million corruption case.
The Percoco conviction was an election-year embarrassment for Cuomo. His opponents say it proves the two-term Democrat hasn't done enough to address chronic corruption in state government, even within his own administration.
Prosecutors sought well over five years in prison for Percoco while the defense said he should get no more than two years.
Cuomo wasn't accused of wrongdoing, but testimony presented an unflattering picture of the inner workings of his office.
In a statement Thursday, Cuomo said Percoco was "paying the price for violating the public trust." He said it should "serve as a warning to anyone who failed to uphold his or her oath as a public servant."
In court papers, defense lawyers wrote that the prosecution "has all but destroyed Joe's life," leaving him facing bankruptcy and prison.
In court, Percoco told Caproni he wanted to "express how sorry I am for my actions."
Outside court, Percoco declined comment, walking away as he was asked if he had remorse.
His lawyer, Barry Bohrer, called it a "difficult day in court" and vowed to appeal.
"We had hoped for better," he said. "We are hopeful that our appeal will be successful."
Assistant U.S. Attorney Janis Echenberg told Caproni that Percoco was known by many as Cuomo's "right-hand man."
"Joseph Percoco wielded immense power and he wielded it behind closed doors," she said.
Echenberg called him Cuomo's "closest adviser, his enforcer" and said getting a call from him was like "getting a call from the governor himself."
"Faith in government may be at an all-time low, and so the court must send a message that corruption will not be tolerated and must be punished," she said.
The judge agreed, saying Percoco's crimes had "reached to the highest level."
"Frankly, it's not surprising that the people of this state have completely lost faith in government," she said, adding Percoco had been motivated by greed and arrogance.
The judge described Percoco as a "corrupt public official with little respect for the law." She rejected part of his defense team's arguments as "unmitigated poppycock."
The scandal didn't substantially hurt Cuomo with Democrats during his primary win over Cynthia Nixon. He won in a landslide.
Republicans pounced on the sentencing, saying the Percoco case showed Cuomo can't be trusted to address Albany's chronic corruption problem. Cuomo's Republican challenger this November, Dutchess County Executive Marc Molinaro, said the conviction and sentencing of a man Cuomo once likened to a brother is an indictment of the administration.
"Andrew Cuomo was sentenced today - he just doesn't have to do the time," Molinaro said. "He came into office promising reform and ended up turning New York State government into a corrupt, taxpayer-paid enterprise that works only to further his presidential ambitions."
Klepper reported from Albany.
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