I ask this b/c my 2 puppies have gunk in their eyes every morning and they scratch quite a bit (though mostly in the morning when they wake up). They dont have fleas (on flea prevention) and are eating Nutro lamb and rice large breed puppy formula. Do you think this might be food related or allergy related?

I'm going to guess neither. As pups, food allergies would be incredibly rare...they're immune systems aren't developed enough to develop allergic responses at this time. Puppies go through lots of problems related to growth (from dandruff, to pano, to eye gunk). Are the symptoms severe, or just little things you're noticing?