I have headaches (above my eyes) which appear when I lie in bed for a long time at night, or in the morning...What could be the causes?

Many possible causes. See your doctor for this. Although this may be nothing serious, your doctor needs to get a more thorough history and perform a physical and neurological exam. If warranted, your doctor may advise a cat scan or MRI of the brain/head. If your doctor can not determine the cause he/she may refer you to a neurologist and an ophthalmologist. See your doctor for this.
?Occipital Neuralgia. Could be occipial neuralgia from neck strain or how you sleep. A headache or pain specialist can do a simple injection (greater and lessor occipital nerves) to see if that takes care of it.
Not an eye problem. That's a weird one. Not an eye problem..Talk to a neuro guy.