Here are a few suggestions that might help. Make sure your son is sleeping at an angle with his head up. If he doesn't use a pillow, you can do this by putting something under his mattress to lift it up a bit where his head usually rests. Also, run a cool air humidifier in his room at night. This will help to thin out the mucous his body is making so that he can handle it better. You can get vapor additives for them, also, that can help with it. Also, both Vicks' and Johnson & Johnson make vapor rubs that are safe for little ones. Try putting a little on him at night. If the congestion is really bad, you can try an old family remedy our family has used for generations. It doesn't sound all that appealing but it really works. You boil a small onion in a pot of water. Allow the water to cool to a temperature that a child can handle. Put the water/juice/broth that has formed into a bottle or sippy cup with a little sugar to sweeten it. Most kids enjoy the taste but the onion will really help to break up the mucous.
You, also, want to talk to your doctor. Ask him if the singular should be making a bigger difference. It may be that he needs to change your son's medication. Not all allergy medications are as effective on all people. You might have to try a few before you find the right one for your son. Sometimes it is not the effectiveness of the medication, though. Sometimes it is just that the pollens are that strong. I'm allergic to early and late trees as well as grass. I don't open my windows during the late spring and the summer when the pollens are very high. We bought a house with whole house air. If you open your windows at night to let in cool air, you may have to look into other solutions such as a couple of room air conditioners or whole house air (if you don't already have it).
Good luck with your little guy. I hope he is feeling better soon.