This line is constantly referred to in the media and even in academic works, yet only secondary sources are ever referenced. Even senior ex-Panthers like Elaine Brown cite it as fact.
My old History professor said that this was actually a common misconception, and that Hoover never said the BPP were the "greatest threat". He didn't give me a source.
So I am stuck and I think this is quite an important distinction to be clear on! Any help in either direction would be greatly appreciated.
This was surprisingly difficult to run down, because it's been so commonly quoted that the sourcing — where a source is even given — essentially becomes an infinite loop. But here goes:
The best primary source I can find for this — the source I actually suspect to be patient zero for the quotation entering the mainstream discourse — is in the Church Committee's 1975 final report — specifically, Book III ('Supplementary Detailed Staff Reports on Intelligence Activities and the Rights of Americans') in the report entitled 'The FBI's Covert Action Program to Destroy the Black Panther Party'.
The quote appears in full on the first page of that report, with a footnote attributing its source as the New York Times of 9 September 1968 — the day after Huey Newton was convicted of manslaughter in the death of Oakland police officer John Frey.
But here's the rub: I can't find that quote in the Times on that day. It's not where I would have expected to find it, in the main news item about Newton's conviction; nor is it included in a story about Spiro Agnew (then governor of Maryland) claiming that student demonstrators were communist puppets; nor does it appear in a small story about gunfire at the offices of the Student Nonviolent Coordinating Committee. It's not, as far as I can see, anywhere on the editorial page, in an op-ed or a letter. I flicked through that edition backwards and forwards, and just couldn't find it.
So, I put the quote into Google News — which has a surprisingly extensive newspaper archive — and found an AP item from 15 July 1969, reporting the Hoover quote in connection with the release of the FBI's annual report for the 1969 fiscal year. Neither the full quote nor any explicit reference to black nationalism appears in Hoover's signed foreword to the report, and while the quote's essential themes (Black Panthers are extremists; Communist influences, etc) appear in the report's section on 'Black Extremism', still no luck on the quote itself.
From looking at other wire service reports around the time of that FBI document's release, it does seem that the quote was widely reported — but its exact source (did Hoover say it verbally to reporters? Was it issued in a press release? Was it included in a report?) appears to vary widely.
At this point, basically out of ideas, Google finally kicked back something really useful: a lengthy footnote (see note 45) in Black Against Empire: The History and Politics of the Black Panther Party, in which the authors went through — in a more laborious and exhaustive way — basically the same search I just did, to try and trace the provenance of the quote. Their essential conclusion is that the quote — or some variant of it — probably did originate with Hoover sometime after the summer of 1969, probably in a press release or media statement, but that its precise origin point remains decidedly unclear.
... here endeth my wild goose chase.