D'Souza didn't say the FBI was the greatest domestic terrorist threat today. That's spin designed to make his views seem extremist. He made a point that the FBI is a greater threat than any militant white supremacist group. Thugs with badges are always more dangerous than thugs without badges.
Of course D'Souza is not an extremist, on the contrary, he is a great patriot!

Bless him.
And yes, he said this:
Dinesh D’Souza: The FBI is a grave threat to our national security. In fact I would say the FBI now poses a greater threat to our national security than any militant white supremacist group. Thugs with badges are always more dangerous than thugs on the street.
Campaign finance violation, felony guilty plea, conviction, and pardon
On January 23, 2014, D'Souza was charged with making $20,000 in illegal campaign contributions to the New York Senate campaign of
Wendy Long and causing false statements to be made to the
Federal Election Commission.
[158][159][160] His attorney responded to the charges by saying his client "did not act with any corrupt or criminal intent whatsoever" and described the incident as "at most ... an act of misguided friendship".
[161][162]
On May 15, 2014,
United States district judge Richard M. Berman rejected the contention that D'Souza was singled out for prosecution, stating, "The court concludes the defendant has respectfully submitted no evidence he was selectively prosecuted."
[163]
On May 20, 2014, D'Souza pleaded guilty to one
felony count of making illegal contributions
in the names of others.
[164] On September 23, 2014, the court sentenced D'Souza to five years' probation, eight months in a
halfway house (referred to as a "community confinement center") and a $30,000 fine.
[27][28] After D'Souza's conviction, his claim of selective prosecution continued to receive support from some
conservative media and commentators.
[165]
On May 31, 2018, President Donald Trump
pardoned D'Souza.
[166]