My 3 yr old has horrible allergies. He has red, puffy, itchy eyes and a runny nose and sneezing. No allergy meds are helping him, what can I do?

Allergists. Please take your baby to see an allergist. An allergist can help identify what allergens are causing all the trouble. It may be possible to eliminate them from the baby's environment. There are a number of prescription medications that may help. And allergy shots, although young children don't like them, are also an option.
See an allergist. In some cases, medications alone (especially when only otc meds are being used) may not be adequate to treat allergies. I suggest you take him to an allergist, who can perform testing to determine exactly to what he is allergic. They can also recommend ways to avoid the allergens, if possible, and may have additional therapies that can improve your child's symptoms.
Eye drops? Most people try claritin, zyrtec, allegra, but eye drops such as zatidor or Patanol (olopatadine) can also help with symptoms. Pollen season is very very tough for many kids right now. Part of the challenge will be to fight through this tough peak of pollen.