There's a difference between the occasional eye booger or tears, and brown goopy eyes, Joey had really bad goopy eyes when we did a food change, they took a while to completely clear up, and I don't know if it was a food allergy or some type of contamination with the food and bacteria. Depending on what's causing it the treatment is different. Here's a good link on causes and cures, but I think a vet check is a good idea:
Tear Staining: The Causes & Cures