Was John F. Kennedy buried at sea?

No, he was buried at the Arlington national cemetery in 1963.

On a related note: JFK was transported from Dallas (after his death) to the capitol in a casket purchased from Elgin Casket Company in Dallas. The casket was only used for his transport and was not the final casket selected for his burial.

In 1966 the transport casket was disposed of in the Atlantic ocean (empty with nothing in it). This was done to discourage its use as a tourist attraction since it served no other purpose and was not considered part of the evidence in his assassination.

JFK had previously discussed possibly being buried at sea, and the choice to dispose of the empty transport casket in a mock 'burial at sea' was a nod to his interest in the custom.

The decision to bury JFK in a national cemetery was to give family and the public a place to pay their respects at his grave.

Coincidentally; John F Kennedy Jr was buried at sea (in 1999) relatively close to the location where his fathers empty transport casket was dropped into the ocean.