Ahmed Ferhani, 27, a mentally ill Algerian immigrant, agreed to serve a 10-year prison sentence offered by state Supreme Court Justice Michael Obus.
Prosecutors had asked for 14 years, but the defense argued Ferhani suffered from documented mental-health issues, including a propensity to cut himself and threaten to do harm to himself, Ferhani attorney Lamis Deek told the New York Post.
Ferhani could have faced up to 32 years if the case had gone to trial and he was convicted of the top terror and hate-crime conspiracy counts against him, the Post reported.
After serving 10 years, Ferhani faces "inevitable" deportation back to Algeria, said Obus, the chief administrative judge for the state court's criminal division.
The sentence is to be executed Jan. 30.
The guilty plea "marks the first time a terrorist has been convicted on state terror charges since the New York anti-terror laws were passed shortly after Sept. 11, 2001," Manhattan District Attorney Cyrus Vance said in a statement.
Terrorism cases are typically tried in federal courts.
"By targeting a synagogue, which I knew to be a Jewish house of worship, in this manner, I intended to create chaos and send a message of intimidation and coercion to the Jewish population of New York City, warning them to stop mistreating Muslims," Ferhani said in his admission of guilt.
Defense attorneys had tried to portray Ferhani as a set-up underling. But surveillance cameras recorded him seeking weapons, calling himself a "mastermind" and "showing great excitement at handling a grenade," the Post said prosecutor Margaret Gandy told Obus.
Ferhani, who prosecutors called a drug dealer with a history of a knifepoint robbery, was captured on a sting tape last year calling Jews "rats" and saying he wanted to grow a beard and side curls to resemble a Hasidic Jew and then sneak into an unspecified Manhattan synagogue and plant explosives.
Ferhani also expressed an interest in blowing up a church in the New York City borough of Queens and the Empire State Building in Manhattan, authorities said.
He and suspect Mohamed Mamdouh, 21, were arrested May 12, 2011, after allegedly trying to purchase weapons, including pistols and hand grenades.
Ferhani has no ties to al-Qaida, authorities said. He once sold cosmetics at Saks Fifth Avenue and later tried to be a fashion model, his father in Queens told The New York Times after Ferhani's arrest.
But Ferhani hated Jews and believed Muslims, especially Palestinians, were mistreated around the world, authorities said.