I believe he saw and photographed something. We had some very interesting things in the air in the late 80s, and the location isn't all that far from either Langley or Seymour Johnson, as well as a couple naval air stations. I don't believe the bulk of his story however. The bit about having called the Pentagon and "talked to the air force general there,” is pure bunk. He'd have been lucky to have talked to a CGO in public affairs. Same thing with statements attributed to "the spokesman for defense at the Pentagon." What kind of reporter would not get names and duty titles if he interviewed DoD officials? And aerial refuelings with probe and drogue systems do occur at altitudes as low as 3000 ft.
The "men in black" thing is a myth, it all started with a joke played on the gullible John Keel by noted ufologist/prankster Gray Barker. Once Keel started talking about them, suddenly others started seeing them.