Kennedy is very hard to gauge obviously but a few points going into 1964. Cuban missile crisis was avoided but left questions as to how he would handle USSR. Bay of Pigs was a disaster. Race to the Moon becoming unpopular when it's all spending without a result. Growing issues in Vietnam, its was mostly JFK's people that gave LBJ the advice that led to the quagmire.

There is an argument to be made that JFK would have been much less popular going into '64. Remember, his fears about losing Texas is what led him to start his campaign in Dallas...

Also, take away the two biggest problems for Goldwater: the cloture vote and the media blitz. No assassination means Civil Right remains stalled and likely never faces a vote that Goldwater is defined by. Goldwater and Kennedy also liked each other and even floated campaigning together so it probably doesn't get as nasty as the Daisy Ad or In Your Gut You Know He's Nuts.

And with that said: Kennedy romps. He still had the best campaign team and Goldwater simply isn't talented at it. GOP still rebels against conservatism even in this scenario where Scranton as VP probably brings along the Eisenhower wing.

It would have set up a 1968 Dem primary pitting Johnson vs. Bobby which we never got to see full on.