Despite his seemingly 'independent' intellectual stance, I.F. Stone may have been revealed by the "Venona decrypts" to be a paid Soviet "agent of influence." This is still disputed by his followers, and I certainly haven't waded through all that stuff, but it has been discussed in various places, such as:
http://capmag.com/article.asp?ID=3010
"...Stone was a highly regarded "independent" journalist and his newsletter was always exposing things about Sen. Joseph McCarthy and others who warned against Communist spies and agents of influence. The problem was that I.F. Stone was a Soviet agent of influence, financed by the Kremlin."
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.