Until I see that sort of thing, I will suspect that this is all guilt by association.
I don't think anyone is accusing Chomsky of denying the Holocaust, although it wouldn't be difficult to find evidence that he downplays the Holocaust to the point of equating Nazi atrocities to America's "war crimes."
The charge is indeed guilt by association, but as the author states in those concluding paragraphs, it is not a casual association. Chomsky writes in clear and knowing support of neo-Nazi organizers in France (Faurisson and Guillaume) who are definitely Holocaust-deniers. Yet because of Chomsky's reputation as a scholar and a darling of the American media and Leftist academia as well as the Left in general, Chomsky is able to deny these associations without fear of losing support.
On the "guilt by association" charge, consider what would happen if someone published a book titled Bill Clinton and the Dixie Mafia. Clinton's supporters -- especially the media and academia -- would first of all laugh down as much of it as they could get away with. No doubt some would find it worth their while to write a response to the book and would probably do so by saying that there is no evidence that Clinton was ever a member of the Dixie Mafia. True enough, but the charge that there was corroboration hasn't been answered just by saying that Clinton was never a member of that group.
In the same way, by saying that Chomsky is in corroboration with Holocaust-deniers and in political agreement with some or most of their agenda isn't claiming that Chomsky himself has denied the Holocaust. But it's a serious charge nonetheless and one that Chomsky's supporters have never answered with anything but arrogant ridicule.
I skimmed through the FrontPageMagazine article referenced above, and I may missed some crucial element, but it reminds me of a recent hit piece "proving" that Edward Said is not really Palestinian because the author strings together some misinterpretations of fact. Here, the article seems to "prove" that Chomsky has "neo-Nazi" connections because 1) he supported the right to free speech of a well-known "Holocaust-denier", Faurisson; and 2) he wrote a prefec to a book by the same person. In neither case did Chomsky himself ever say "I deny the Holocaust occurred" but rather something like "everybody has a human right to free expression" even if repugnant.
Here's why this point is absolutely crucial. If, as Chomsky's critics allege, he is evil because he affirms the right of even a denier of the Holocaust to express his views, then what is one to call those people at the very highest levels of the government of the state of Israel who deny the Holocaust? Does the question strike one as absurd? Well, in fact, it has been official Israeli government policy (at least since the official military alliance with Turkey dating from 1958), to deny the reality of the Armenian Holocaust of 1915, when the Turkish military killed half of all Armenians; and later of the 1922-1923 Greek Holocaust when massive numbers of Greeks were killed or driven from Asia Minor by the successor Turkish government under Ataturk.
Chomsky has mentioned this in several books I have read, and his doing so is what got me started reading other of his books. So I think the issue of "Holocaust denial" cuts both ways. WHICH Holocaust; who benefits from denying the one ot the other? I see Chomsky stating that BOTH happened; his political enemies claim only ONE happened. Who is closer to the truth?