You also should try an antihistimine eyedrop. Rx Patanol is the one the works the best for me. But Opcon-A is an OTC one that works great also. I find it also helps to dab a little of the eyedrops on the puffy bags below my eyes to shrink them. When the pollen count is really high, I use an eyewash to wash the pollen out of my eye. If the puffiness is worse in the morning, I agree it could be sinus related, but allergies to dustmites could also be causing you to wake up with puffy eyes.