I have had the same thing for 7 yrs and not been able to figure it out. The frequency of the vibration has slowed over the yrs and it seems to be related to the dose of Vitamin D I was taking. Since cutting out Vitamin D supplement it has virtually disappeared. I noted another person felt it was related to obstructive sleep apnea but I am not sure about that as I do not have it , at least in any severity according to testing but some nights might be different than others. It only happens to me as you say when you are just waking up in the night or it might be that it wakens me but never when I am fully awake or in the day. There is also another thing that can cause body vibrations but these are not the same and of much lower frequency and that is natural sources of licorice such as the DaraLea brand. You will notice the vibration the same way either falling asleep or waking but it is usually within 24 hours of eating the licorice and cutting it out stops it from happening again. If anyone has found a cure for the other vibrations other than Vitamin D as a cause, let me know. These vibrations are not due to stress or anxiety.