The bodies, landed just before dusk, were taken for examination by state coroners before being returned to the Kennedy and Bessette families.
A memorial service will be held for Mr Kennedy, 38, and his wife at the small St Thomas More church in Manhattan tomorrow. President Clinton and Hillary Clinton will attend.
The breakthrough in the search came late on Tuesday when a remote-operated submarine, lowered from the USS Grasp, a salvage vessel, located the wreckage. Video pictures from a camera on the submersible relayed to the Grasp showed the figure of Mr Kennedy inside.
Yesterday morning divers found all three victims in what was left of the Piper Saratoga plane which was on its way from New Jersey. The impact of the crash had ripped the wings and the engine from the fuselage.
Soon afterwards, Senator Edward Kennedy was taken by helicopter and boat to the Grasp to witness the last stages of the recovery effort.
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