Gooden's black 2012 Chrysler was pulled over around 11:10 p.m. Monday near Ferry and Vincent streets in the city's Ironbound section, Public Safety Director Anthony F. Ambrose said.
EMS was called to evaluate Gooden, 54, of Piscataway, before he was taken to University Hospital in police custody, Ambrose said.
"Doc" Gooden unanimously won the National League's Cy Young Award with the Mets in 1985 following one of the most historic seasons ever by a pitcher -- going 24-4 with a 1.53 ERA and 268 strikeouts.
A year later, "Dr. K" and the Mets won the World Series.
Gooden won two more championships with the Yankees -- in 1996, when he also pitched a no-hitter for the Bronx Bombers, and again in 2000.
This is the second time in less than seven weeks that Gooden's been busted in New Jersey.
Police in Holmdel said he was DWI and carrying cocaine when they stopped him on June 7.
"It's sad to see the continued problems of this former star," Ambrose said, "but it's an example of the persistent scourge or drugs and alcohol in this country and the stranglehold they have on addicts."
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