I emailed Fred Shapiro, the editor of the authoritative Yale Book of Quotations, to ask him about the TMRC dictionaries. He replied:
"I am familiar with the 1959 occurrence of "hacker," which has been confirmed. The problem with it is not that it is unconfirmed, but rather that it is a general usage not a computer usage. For that matter, the 1963 usage that I discovered is also not specific to computers, although I believe that phone-hacking is pretty much the same phenomenon as computer-hacking. The earliest usage I am aware of that is specific to computers is dated 1968.
But the real issue here is whether "hacker" originally had malicious or benign connotations. Since the general usage of "hacker" in MIT culture is clearly the ancestor of the computer usage, as soon as the 1959 citation was discovered I conceded that I was probably wrong about "hacker" originally having malicious connotations.
Fred Shapiro, MIT Class of 1974"