The collection includes a Lyndon Johnson signed copy of the famous photograph Stoughton took of Johnson being sworn in as president aboard Air Force One after Kennedy was killed.
There is also a picture of both Kennedy and his brother Robert with Marilyn Monroe.
"One of the photographs in the collection is what we believe to be the only image to show Marilyn Monroe with John F. Kennedy and Robert Kennedy, and she had come straight from singing 'Happy Birthday Mr. President' at Madison Square Garden," said Matthew Haley, a book and photography specialist at Bonhams.
Stoughton's family decided that now, 50 years after Kennedy was elected president, is a good time to pass the pictures on to collectors.
