This recommendation may sound crazy to you at first, but please hear me out. Buy a Neil Med Sinus Rinse Kit, and rinse your son's sinuses when he gets up in the morning. You can buy the kit at Target, Walgreens, CVS, etc.; maybe even your grocery store (mine sells it).
I'll tell you about my experience with it before I tell you more about the kit (in case you don't know). I have a 5 year old daughter with a medical condition called Cystic Fibrosis which affects the mucous membranes throughout her body. Her doctor recommended that I rinse her nose (and mine whenever I need it) to get the mucous out and keep sinus infections at bay. Well, was I impressed!!! I also have a 2 1/2 year old, and I rinse her sinuses too because she kept getting ear infections and nasty colds. She was frightened at first, but when she saw what came out, and she found that she could suck her thumb comfortably afterward, she too was impressed. She was still frightened, however, but at the same time wanted to do it (like jumping off of a diving board for the first time). For a while, I had to wrap her tightly in a towel to keep her hands out of the way, hold her over my knee, and basically wrestle with her, but now, she asks me to do it. She'll walk into the bathroom, but her little blanket on the counter, and lean over the sink. Mind you, I HAD to do this to keep the family healthy. It was stressful at first. But, I'm totally sold on it and can't figure out why I'm only now finding out you can do this. It just makes sense.
I do have some tips: 1) Yes, you'll feel like your eyeballs are swimming, but you'll get used to it, 2) use fairly warm water, but certainly not hot. It will be much more comfortable than cool water, 3) plug the sink so that you can see the color and amount of mucous your son has and determine if he has an infection, 4) Try to be exact in your water measurement to keep the solution from stinging, 5) try not to be grossed out, 6) keep doing it!
My little one coughs until I rinse her nose in the morning, and then she's good for the day. It's also cut her incidents of ear infections and colds by more than half.
Now, for what it is. Basically, it's an 8oz. squeeze bottle. The kit comes with premixed packets of baking soda and potassium. You mix a packet with water in the bottle to get saline which is much more gentle on your sinuses. If you used plain tap water, if would sting really bad. There is a pediatric version, with packets measured for 4 ounces, but I found that I had to rinse her twice, so I switched back to the 8oz.
I hope this was helpful to you! Good luck.