Based on the link posted by BCdotWEB: the first instance of the word Krytonite is in episode 218 "Visitor"—several episodes after Clark meets Virgil Swan, who informs him about his Kryptonian origins.
A transcript of the episode reveals the relevant dialogue (which occurs at around 26:30 on the DVD):
Pete: Well, if you really want to know [whether Cyrus is Kryptonian or not], I could go up to him with a piece of meteor rock.
Clark: No, it's called Kryptonite.
Pete: Kryptonite. Is that with a C or a K?
At this point in time, the following characters know about Clark's Kryptonian identity: Clark, Virgil Swan, Pete, Jonathan, Martha, and Jor-El (and perhaps some of Swan's staff), any of whom could have been the first to use the term off-screen. His response in the above quote suggests that the term was not coined by Pete, and it seems most likely that Clark was the first to use it.