The people involved in the Army-McCarthy hearings were innocent, just for starters. Where do you think that "do you at last have no sense of decency" comment came from?
McCarthy did great damage to conservatism. He fired a ton of buckshot, most of which missed the target and hit innocent people.
Nixon going after Hiss via HUAC (of which he was just a member, but the key investigator) was far more effective. It was targeted toward someone against whom there was clear evidence.
Nixon made a lot of enemies due to the Hiss hearings, but he didn't undermine the anti-Communist movement in the process. Rather Nixon proved something that McCarthy was never able to prove, the existence of Communists in high positions in Washington.
McCarthy used generalities ("I have here a list") and rarely had the evidence to support the charges. Yes, he was onto something. But with his wild accusations with minimal evidence, he hurt the cause. A more careful Senator would have rooted out the Lattimores and so forth instead of leaving them painted as victims for several decades.