H.W.
Be careful of any OTC allergy medications. When we put my son on Claritin (he's nearly five), I read a lot of reveiws. There were some concerns about behavior (manic, screaming, nightmares) with some two year olds.
Probiotics may help. Pediatric chiro might help if it's not an allergy. There are a lot of bugs out there right now, so you might want to consult with your pediatrician first. They should be able to inspect the ears, nose and throat with a scope and figure out what's going on.