One night she even woke me up after I was asleep. I find it disgusting to hear her moans of passion as she plays with herself. You can always take more drastic measures later. Of course, sex can be much harder to talk about because it's personal and private. To her credit, your roommate does wait until she thinks you're asleep before she goes at it.
People sometimes masturbate as a way to release tension or fall asleep.
If dropping hints doesn't work, you could be more direct with your roommate. Perhaps you feel that your privacy is being invaded. Or if you are disgusted by masturbation, you might want to read about female sexuality and the functions of masturbation. Also consider sexual words that you're comfortable using, or any metaphors that will let her know that you're awake and offended. Practice a few different lines beforehand so that you're comfortable when you start the conversation.