Brief Answer:
Migraine vs recurring sinusitis.

Detailed Answer:
I read your question carefully and I understand your concern.

Let me start by saying that it shouldn't be anything serious. Yes it can happen at times for a CT scan to miss something, but I don't think that is your son's case. His headaches have started since almost two years, so CT scan was performed after over 18 months and serious brain involvement of any kind would have had plenty of time to grow and become visible on CT. Also it would be a persistently growing headache not in the form of attacks as you seem to be describing.

The two most probable reasons which could be causing headaches corresponding to your description are migraine or recurrent sinusitis.
Migraine while more frequent in adults is also often found in children. Treatment consists in medication to address the pain like over the counter painkillers acetaminphen, ibuprofen, naproxen etc. It is important to realize that they should be taken early in the course of the headache, don't wait until pain reaches its peak. They could be accompanied by antiemetics (anti vomiting drugs) like Perchlorperazine. There are formulations containing painkillers with antiemetics in the same pill as well.
If patients have frequent headaches (over two attacks a month) regular prophylactic treatment is considered.

The other possibility is recurrent sinusitis. That is the most likely diagnosis if your son has also nasal discharge, nasal congestion, feeling of pressure and pain in the face etc. Also if the pain persist it is also more likely as a migraine attack by definition lasts less than 72 hours (in children usually less). If that is the cause nasal decongestants and antihistaminics to facilitate evacuation of the sinuses are the first measure. Painkillers for headache (acetaminphen, ibuprofen) can be taken to alleviate the pain. If persistent for several days or in case of fever another course of antibiotics may be needed. Also in recurrent chronic cases it must be looked about predisposing causes like nasal polyps, allergic conditions which can be addressed.

I hope to have been of help.

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Brief Answer:
Sinusitis is more probable.

Detailed Answer:
Those symptoms could be consistent with both alternatives. Vomiting while more frequent in migraine can be caused by sinusitis due to the post nasal dripping which you yourself suggested. Migraine apart from headache with nausea and vomiting is often accompanied by photo and/or phonophobia (increased sensitivity to light or noise) while sinusitis has the nasal discharge. However the lack of those features doesn't exclude the diagnosis so it can be difficult to distinguish between the two.

The length of the attacks in time and presence of residual symptoms in between, is a good indicator. The shorter a time course these attacks have, being free of pain in the intervals between them, the more likely they are to be migraine attacks. Meanwhile if they are persistent, over 48-72 hours, or are relieved but only partially, then sinusitis is the likely cause.

I remain at your disposal for further questions.

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