It's easily possible that Hermione has seen at least one picture of Sirius (she mentions him by name as the Potters' betrayer in Chapter 8), and given her memory it would be plausible for her to recognize him, even months afterward. Additionally, Sirius is one of the few people who would cause an immediate reaction of terror at first sight.

Another one might be - bear with me here - Lucius Malfoy. This idea is a little shakier, as it's less plausible that Hermione is familiar with his appearance, but the advantage is that it neatly accounts for the otherwise-strange

The black mist darkened and lightened, like a shake of the head. "I am frightened of Harry Potter," it whispered. "Of the coldness in his eyes, of the darkness that grows behind them. Harry Potter is a killer, and anyone who is an obstacle to him will die. Even you, Hermione Granger, if you dare truly oppose him, the darkness behind his eyes will reach out and destroy you. This I know."

since Lucius seems to be convinced Harry is possessed by Voldemort. (Though it casts a certain odd light on Mr H&C's warning to Hermione about Lucius, I think it's at least possible that he could bite his tongue enough to say "though you are Muggleborn, you possess a power of wizardry greater than any pureblood" if he considered it just a flattering lie.)

The obvious antipathy toward Dumbledore and knowledge of Snape serve equally well as evidence for Lucius or somehow-evaded-going-to-Azkaban!Sirius. Interestingly, they also work for Pettigrew, who Lupin tells us "adored secrets," but who presents the issue of Hermione almost certainly not recognizing or being terrified of him.

Of course, the only reason to entertain such out-there possibilities is how weirdly clumsy and out-of-character this latest act would be for Quirrel. Mr H&C's first appearance (in Chapter 35) is really obviously Quirrel, if for no other reason than

Chapter 35: Mr. Hat and Cloak gave a whispery chuckle. "Indeed," said the whisper. "With the murder of one student five decades ago being the exception that proves the rule, since Salazar Slytherin would have keyed his monster into the ancient wards at a higher level than the Headmaster himself."

Chapter 49 (Quirrel): "First, I believe the Chamber of Secrets is real, as is Slytherin's Monster. Miss Myrtle's death was not discovered until hours after her demise, even though the wards should have alerted the Headmaster instantly. Therefore her murder was performed either by Headmaster Dippet, which is unlikely, or by some entity which Salazar Slytherin keyed into his wards at a higher level than the Headmaster himself."