Kovarian

The Eye Patch Lady was a mysterious woman, of whom Amy Pond had recurring visions. She wore an eyepatch or a similar device over her right eye.

The first time Amy saw her was whe she appeared at the little girl's bedroom door at Graystark Hall Children's Home. She appeared through a hatch in the door, which later disappeared. Amy was startled by the woman and asked who she was, but the woman ignored her and said "No, I think she's just dreaming" to someone inside the room. When Amy entered, the room appeared to be empty, with no evidence of the woman or the hatch. (DW: Day of the Moon)

While asleep on a pirate ship, Amy was woken by a noise and saw the woman in a hatch that opened on the hull of the ship. She said, "It's fine. You're doing fine. Just stay calm", and then she vanished instantly, along with the hatch. (DW: The Curse of the Black Spot)