Two plastic baggies allegedly containing cocaine were found in the 54-year-old Gooden's auto.
Prosecutor's spokesperson Christopher Swendemen told the Post that Gooden was pulled over for driving too slow on a highway and failing to maintain his lane and having overly tinted windows.
Gooden was charged with third-degree possession of a controlled risky substance, possession of drug paraphernalia and being under the influence at the time, and driving under the influence.
He also was ticketed for driving under the influence, which is a municipal offense.
Gooden, 54, has a lengthy arrest sheet and has battled substance abuse since his playing days.
The 1985 Cy Young Award victor has struggled with drug and alcohol addiction over the years.
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Last month, Gooden posted a picture of himself at a rehab facility in his native Tampa, along with the caption: 'I had a great time speaking at Villa Veritas.
The New York Post was first to report on the criminal charges in a story published Friday.
He was suspended from baseball for part of the 1994 season and all of the 1995 season after testing positive for cocaine.
Later, after making a comeback and winning two World Series rings with the crosstown Yankees, Gooden was arrested in New Jersey for driving under the influence and crashing his auto while driving his five-year-old son Dylan to school. He served prison time in 2006 for violating probation and charged with a DWI in 2010.
The ex-pitcher won the National League Cy Young Award while with the Mets in 1985 and was a member of the Mets' 1986 World Series championship team. He finished his 16-year career, which included stops with the Yankees, Indians, Astros and Devil Rays, with a 194-112 record with a 3.51 ERA.
He also threw a no-hitter with the New York Yankees in 1996.