The FBI have confirmed the remains were reputed mob hitman William Cutolo, Sr.
The Suffolk County Medical Examiner ruled the cause of death as homicide.
Police stood guard at the site as the digging continued on Tuesday.
FBI agents on Long Island have been digging at three wooded sites since last week.
They were pointed to the site in East Farmingdale by a Colombo crime family informant. The informant said there are three bodies buried there.
Cutolo disappeared in 1999 on his way to meet the, then Colombo boss, who was convicted last year for ordering Cutolo's murder.
Investigators are also looking for the remains of 21-year-old college student Carmine Gargano Jr. and another Colombo crime family member -- Colombo family associate Ralph Greaves.
Two small backhoes were complemented Wednesday by a team of about a dozen law enforcement officials, some of whom had "FBI Evidence Response Team" written on their shirts and jackets. On other days, investigators have removed tree branches, sifted through mounds of dirt, and shut down local streets, drawing curious looks from local business owners.
The search could end up having ramifications for other mob cases.
Attorneys for two men convicted in the killing of Cutolo, a reputed Colombo crime family underboss, have told a federal judge they will seek a new trial now that his remains were found. They say that the discovery runs counter to the argument by prosecutors that he was dumped in the ocean.
"Clearly, this new evidence directly contradicts the theory on which the government proceeded at trial," attorneys Sarita Kedia and Robert LaRusso wrote to the judge.
Neither FBI spokesman Jim Margolin nor Robert Nardoza, a spokesman for the local U.S. Attorney's office, would comment on any specific aspect of the investigation.
Cutolo vanished in 1999, when he was 49. Reputed acting boss Alphonso "Allie Boy" Persico and accomplice John "Jackie" DeRoss were convicted last year of orchestrating Cutolo's killing.
Prosecutors said Persico feared Cutolo was going to seize control of the crime family from him.
They are scheduled to be sentenced for their roles in the Cutolo killing in December, although their attorneys say the new revelations merit a postponement until the latest investigation is closed. U.S. Attorney Benton Campbell confirmed the identity of Cutolo's remains in a letter to the judge who will preside at the sentencing.
One of other victims suspected of being buried there is former Pace University student Carmine Gargano Jr. He was 21 when last seen in July 1994. Authorities were told he was killed in a revenge plot targeting his cousin, a reputed member of a rival crime family.
Authorities also reportedly believe reputed Colombo associated Richard Greaves may be buried at the East Farmingdale site. He was killed in 1995 because bosses feared he might become an informant.
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STORY BY: Eyewitness News reporter Jamie Roth
WEB PRODUCED BY: Lakisha Bostick and Bob Monek
