If you still have tonsils or adenoids...that could be the problem. I just had a tonsillectomy and adenoidectomy and they were causing some major ear issues....infection after infection...as well as having tonsilitis and the such. Not fun!
It's winter and you probably have the heat going in your house, depending on where you live. That causes the air to become really dry and it can make you wake up with a sore throat and/or ear (because the eustacian tube also dries up in dry air situations).
You should buy yourself a humidifier and run it overnight while you're sleeping and see if it helps. It made a really big difference for me.