JZ, I suffer from the same sort of thing -- bad allergies in the springtime and my running suffers, too! I started taking allegra (not allegra D) and it really helped me tremendously. I take it during the spring when everything is blooming, and it hasn't affected me.
You should definitely get tested to find out what you are allergic to. I could never run at Stanford because I am allergic to eucalyptus (sp?) trees. Whenever I ran near these trees, my chest would feel like I had a rock in it, I would get fatigued very easily, and also have burning eyes, and itchy skin. It is frustrating, especially when you are in shape.
You could also get allergy shots, but I wouldn't recommend this unless you are living in a particular place for a long period of time.
My advice would be to see a doctor. A simple drug like allegra or claritin might work for you, but look out for side effects.