I gave my cat the Feline leukemia vaccination and now her eyes are watering ALOT ?

Watery eyes in not a symptom of an allergic reaction to the shot. Trust me if there was an allergic reaction to the shot you would definitely know it. Most reactions to shots are alot more serious that watery eyes. Since your cat already has allergies and you stopped giving her the allergy medicine it seems logical that it's her allergies acting up.