It's really very hard to say, even in hindsight, because the political climate of the time created so much misinformation and suspicion. Since the 1920s and the first Red Scare, communism had been something of a taboo in the US public sphere; the Communist Party of the USA was treated as a subversive organisation by the FBI for a large chunk of the 20th century, and CPUSA membership was (for many people, at least) something to be concealed or denied.

Certainly, McCarthy's notorious claim of 200+ known communists in the State Department — a number even he didn't stick with for long — is rightly derided as totally unsubstantiated nonsense. It was could have been lower; it could have been higher. We just don't know — and neither did McCarthy.

There's also a problem of definition here: what is a communist? People's political orientations are not fixed or permanent; many of those accused of being communists during the McCarthy witch-hunts were in fact being accused of once having been communists — or even just having associated with communist groups in the past. Arriving at an actual number is probably impossible, simply because you can't establish a reliable set of criteria for the definition.

There were communists in the State Department, but the ones we know about are generally those — like Alger Hiss, Julian Wadleigh and Laurence Duggan — who were revealed to have spied for the USSR. It's perfectly reasonable to believe that there were other communists or fellow travellers at State who were totally loyal, and whose names we don't know. Because really, why would we?