This strikes me as difficult to assess because he was cut down in death before the full picture of his policy and effectiveness could be realized. One such area was civil rights. How would what he began in 1962 in Alabama at the University of Mississippi have played out over time had he not been violently removed from office?
I do think he was a great President, but I also think he has been lionized in death, and few remember that he was only President for less than three years. We didn't get to see much of who he would have been as President outside of the Cold War policies he pursued and the beginnings of his involvement in civil rights. He probably would have gotten us involved in Vietnam as Johnson later did and this would likely have tarnished his image in history.
Kennedy might have been a great president. People expected great things from him, but he was killed before he could accomplish them. Let's face it, he was young and good looking. His family had great fashion sense. We liked him, and he inspired us to have faith in the presidency. That does not make him a political genius.
Kennedy's presidency could not be qualified as great. Many of the big moments of his presidency were reactive instead of proactive. The Bay of Pigs is one example. Another example is the civil rights movement. Kennedy's actions toward this were a result of the very publicized children's movement in Montgomery. Kennedy really had no action until the pictures and newscasts of children being arrested by the busload, or being thrown to the ground by fire hoses became public. Could he have been a good and effective leader had his presidency transcended the infancy stage? Possibly.
It seems that he is famous because of his early death and his manner of death rather than precisely through what he achieved. I tend to think of JFK as a President who, like all Presidents, promises a lot, but because of his early death never was given an opportunity to show if he could deliver or not. Certainly the Cuban Missile Crisis could be considered a high point, though recent revelations about his private life, his sex addiction and drug use should make us worry about somebody holding the power of live and death for the known world.
Kennedy was more or less placed into office by his father, whose energies and resources had long been directed toward getting one of his four sons into the White House. John Kennedy was only in office a thousand days, but during those thousand days, he brought the nation back from the brink of nuclear war, so I will at least argue that he showed enormous leadership during that near catastrophe. During the dark days of the Cuban Missile Crisis, days when America held its breath, Kennedy watched and listened, yet refused to act with any sort of impulsiveness; one hallmark of Kennedy's style was that he valued diversity of opinion, and welcomed it when considering an important issue. There was much pressure from his military advisers to "fish or cut bait" in regard to the Russians, but Kennedy insisted that it was more important to not blow up the world than it was to show the Russians how tough America was.
This is, of course, completely a matter of opinion. I would not say that Kennedy was a great president because I do not believe that he really accomplished anything of great note.
The main thing that JFK accomplished was to "win" the Cuban Missile Crisis. It was certainly a great thing that he helped end that standoff without violence. On the other hand, he was also the president who got the US more deeply involved in Vietnam, and that was certainly no triumph.
On the domestic front, JFK really did not accomplish much. This is certainly true when you compare his record to that of Lyndon Johnson, who actually did manage to pass a lot of important bills in areas where JFK really did not do much.
I think JFK's reputation as a great president is due mainly to the "Camelot" image of his time as president. This is an image based mainly on his (and Jackie's) youth and good looks, not on his actual accomplishments.