The most sure-fire way to get a good homeopathic remedy is to take your son to a homeopath. But the remedies are safe and free of side effects if you want to try self-prescribing.
Educate yourself by googling "homeopathy for children," and add the specific symptoms you want to control. There are a few different remedies that can be helpful for allergic symptoms, and any remedies recommended for children won't have side effects (unless he's allergic to milk, because the little pellets are made from milk sugar).
Several websites will help you choose which remedy will probably work best, though it's sometimes neccessary to try two or three to get a good match for a particular person. The trick is to match the remedy as closely as possible to the symptoms. But since the remedies are only about $7 each, you're not out much if you have to try two or three.
Homeopathy works for about 8 out of 10 people, is inexpensive, and most common remedies are available over the counter at many health-food stores and pharmacies. They are easy to administer to a child, 1 or 2 pellets melt under the tongue take effect in minutes if they are going to work at all. If not, you can try a different remedy with possibly better results.
I personally use Histaminum Hydrochloricum for itchy eyes, runny nose, sneezing, and hives. Reliably stops my symptoms cold.
Good luck – I hope your find a solution that works for your little guy.