We do not know for sure. Here are the quotes:

from chapter 6

As his hand touched the back door's handle, he heard a last whisper from behind him.

"Hermione Granger."

"What?" Harry said, his hand still on the door.

"Look for a first-year girl named Hermione Granger on the train to Hogwarts."

"Who is she?"

There was no answer, and when Harry turned around, Professor McGonagall was gone.

from chapter 8

"Were you told to wait for Harry Potter on the train to Hogwarts, or something like that?"

"No," Hermione said. "Who told you about me? "

"Professor McGonagall"

It doesn't look really like her style though.

The narration in the passage is extremely suggestive that someone other than McGonagall was at work. Dumbledore and Quirrell used to be the main candidate hypotheses for who it was, until this chapter basically confirmed it was Dumbledore.