In current usage, crony is a negative term used to refer to a partner in crime or who aids you in other misdeeds. This is a recent development in meaning, and through most of the word's history is has been positive in tone.
“Jack Cole, my old school-fellow ... who was a great chrony of mine”.
-- Samuel Pepys, 30th of May 1665.
Crony first appeared as a bit of college slang at Cambridge in the 1660s. It was apparently coined as a form of the Greek khronios, meaning 'long-lasting', and it referred to a particularly close or old friend. For a period in its youth it was also used to mean 'lover', as in John Adlar's 1671 poem Fruit of That Forbidden Tree; "She that for love with her crony lies / Is chaste: But that's the whore that kisses for prize."
The pejorative sense appeared in 1952, when the New York Times, in referring to the Truman administration, wrote "The amount of politically entrenched bureaucracy that has earned for Mr. Truman’s regime its sorry reputation for corruption, cronyism, extravagance, waste and confusion". It has continued to be used on this sense ever sense.