In Secret Avengers #1 (2013), S.H.I.E.L.D. works to bring down Andras Bertesy, a Hungarian arms dealer also versed into dark arts. The guy is reported to want to sell teleportation energy to Al-Qaeda cells, which would enable them to teleport into any building (say, the White House).
A deal takes place, with a "high-value American target" at stake. Skip some panels, a terrorist teleports into the Oval Office, only to be greeted by Nick Fury shooting at him. Now as the guy isn't formally introduced, I cannot 100% guarantee he is indeed Al-Qaeda, but given the above dialogue and his rather stereotypical look, he probably is.
It's a tad bit "cheating" as the comic is a movie tie-in, but in Avengers: Infinity War Prelude #1 (2018), Sam, Steve and Natasha retrieve Chitauri-fueled weapons from terrorists; a truck bearing ISIS' flag (or something really close) is briefly shown.