My Boxer sometimes shakes his head like a bobble head

Does it look like this? Video

If so, I wouldn't panic, but instead start keeping records of when he has them, what he has eaten, what activities he does beforehand, etc. Keep a log. And then when you visit the vet, talk to him about it.  

Many boxer owners report that their dogs have episodes of what are described as "head tremors." They are not seizures, and do not seem to affect the dog's attitude or behavior in any way. They often begin while the dog is still a puppy, and happen intermittently (often very rarely) throughout the dog's life. Usually, they occur when the dog is relaxed or sleeping.

Veterinary examination of these dogs finds no association with hypoglycemia, seizures, epilepsy or any other identifiable condition. While observation of head tremors can be disturbing and frightening to the boxer owner, take comfort in the fact that they do not seem to shorten the dog's life, interfere with his activities or cause any consequent problems whatsoever.

Source 

Just to offer  (ask for) some clarification.  I think you are stating this happens when your dog is relaxed.  If the dog is focused or interested and it is occurring, those would be intention tremors.  Intention tremors are the result of neurological insult.  Some dogs do just fine, others do not.  As to inability to stablize the head when relaxed appears to be muscle tone in the opposite directions (not enough).  I agree monitoring closely.  If at all possible, keep a video diary so you have a good baseline.