The author of that article didn't support that statement with a single fact, resting on the implication that publishing criticism of McCarthy was enough to mark a person as a "Soviet agent of influence" (and since he sold a newsletter that contained such criticism, therefore he was "paid" for doing the will of the Soviet government).
Granted, I have no idea what nasty secrets of the Cold War still lie buried and unearthed. Still, I doubt that Stone was a Soviet spy. Stone was opposed to McCarthy's and Cohn's bullying tactics - however that doesn't necessarily make a person a Communist.
Stone's reporting was reknowned for advocating for the little man, the powerless individual. He was vigorously opposed to government tyrrany, and strongly supported democracy and the Bill of Rights. I sincerely doubt he'd have supported Soviet totalitarianism.
The U.S. Senate eventually condemned Sen. McCarthy for "conduct contrary to Senatorial traditions".
The Chief Counsel of the U.S. Army said to Senator McCarthy: "Until this moment, Senator, I think I never really gauged your cruelty or your recklessness. Let us not assassinate this lad further, Senator. You have done enough. Have you no sense of decency, sir, at long last? Have you no sense of decency?"
Muckracking reporters make enemies, and that unfounded allegation smells like the sort of tar people smear on their enemies.
The bitter irony is that posthumously it turns out that Sen. McCarthy was actually correct in some (but nowhere near close to all) of his accusations, especially concerning Communist infiltration in the Department of State. McCarthy was like a shotgun blast that managed to hit some of the correct targets, but with a LOT of collateral damage.
re: I.F. Stone and the Venona decrypts
As I said, I haven't waded through all the relevant material, but IF someone is referred to repeatedly in those decrypts as a paid Soviet agent that is not an "unfounded allegation" but evidence right from the horse's mouth of the head of the Soviet spy network in North America, communicating with their bosses in the Kremlin. The challenge is that such decrypts refer to agents by code names, so of course one has to figure out from context (or know from other sources) who agent 'ALES' is, etc. Because of the code names involved, apologists for various Soviet spies and agents of influence can hold out forever claiming there is uncertainty about who a certain code name referred to, but often there is a lot of evidence from the types of information referred to, etc.
As for McCarthy, he was right far more often than he was wrong, but I would say that he certainly could have been more careful. Still, it is McCarthy who has been smeared and slandered worse than just about anything he was ever accused of.....if you read the actual transcript of that Army hearing where the lawyer wailed "at long last, etc." you can see that the lawyer was grandstanding the way that idiotic liberals like to do.