No way anybody beats Kennedy in 1964. Not Rockefeller, not Goldwater, not Nixon. The only Republican candidate who the Kennedys were scared of was George Romney, but he took himself out of the running for '64. As for Nixon, had he won in 1962 as expected then he'd probably be put forward as a compromise candidate in 1964 and win the nomination. The problem here is that in 1962 he promised not to run for President, the Democrats would use this to show "Tricky Dick's" dishonesty and it would cripple him in the general election. In 1964 the economy was good and the country had just come off JFK's successful handling of the Missile Crisis and the Nuclear Test Ban. Had JFK survived, then in 1964 he'd be leading the bipartisan effort to pass the Civil Rights Act. The political winds would be at his sails and he'd be re-elected. At that point Nixon's national career is over, and I imagine he'd be unpopular in his home state too for breaking his promise not to run for President in 1964.
Against LBJ, Nixon would be utterly crushed. FWIW, in his memoirs Nixon said that if he'd won in 1962 then he'd have been drafted to run in 1964, only to become a second "Tom Dewey" and lose twice in a row. With Nixon out of the picture in 1968, I imagine that Rockefeller would be the party establishment's choice and he'd cruise to victory over Humphrey.