According to JKR's inteview answer, it's implied that Dumbledore was aware, because he let it continue on purpose (pedagogically, not just maintain-Snape's-cover reason):
Q: Why does Professor Dumbledore allow Professor Snape to be so nasty to the students (especially to Harry, Hermione, and Neville)?
JKR: "Dumbledore believes there are all sorts of lessons in life ... horrible teachers like Snape are one of them!" (Yahooligans! chat, 2000)