Seems tough to nail anything down, true or not. Know how to access the NYT's achieve?
"The first attribution of this quote to President Kennedy comes from a story in the April 25, 1966 edition of the New York Times.
So did Kennedy say it? Possibly. The only attribution we have is an anonymous source from the Kennedy administration by a New York Times reporter three years after Kennedy was assassinated. I’ve found no record that pre-dates 1966. It’s not exactly like he said it in a public speech or even to a reporter directly."
https://paleofuture.gizmodo.com/the-story-behind-that-jfk-quote-about-destroying-the-ci-1793151211
Kennedy made extensive use of the CIA in Vietnam. The only time he is known to have bitched about the CIA was over the botched Bay of Pigs invasion, but that was mostly Kennedy’s own fault. He had been given a good plan by Eisenhower, who knew plenty about how to run a successful invasion, but Kennedy cancelled the air cover, among other things.