Unless your uncle and his daughter tested at a flaky lab with a bad reputation for accuracy, a positive is definitive. Another test, between her and your father, would indicate your father is not the dad. It would be conclusive. Brothers do not have the same DNA. (Unless they are identical twins, which your dad and uncle are not.)
Marcus Gunn lazy eye is genetically linked, which means not just that your dad could pass the genetic tendency on (which everyone seems to be focusing on here, probably because it's so noticeable) but also that your grandparents passed the tendency to your dad and to his brother. A family tendency is just that, it means your cousin got it from up the bloodline. (In fact, if her mother had been hanging around with a totally different guy than your father when your uncle was away, the fact that her daughter got Marcus Gunn would be conclusive evidence that her baby came from your uncle.)
If you think there is any chance your cousin and her dad tested at a cheapie so-called lab that advertises heavily on the Internet and has a bad reputation, there is some possibility of a false result, and they might want to test again with Ravgen or the DDC. But if they used a reputable lab, there is no reason to question the results. If you, yourself are uncomfortable with this and would like to be a thousand percent sure and your cousin and dad are willing to play along, contact one of those two labs and have your dad and cousin do a test. Your dad will not come up positive just because his brother did, he and his brother have entirely separate DNA.