The better choice is "with". You would be understood using "in", but it is not common usage. However, a manufacturer of eyeglasses, when asked occupation, might say, "I am in glasses."

You would say either 'The girl with glasses is my cousin' or 'The girl wearing glasses is my cousin'. The use of 'a pair of' sounds very unnatural here. This is the same construction as 'The girl with long hair' or 'The man with a moustache'. 'In' is only used for clothing e.g. 'The girl in a blue dress'.

You use "in" for something that wraps around you and that you are actually inside: "The man in the grey flannel suit," "The woman in white" (here, "white clothing" is understand), "a wolf in sheep's clothing." You use "with" for something that you are carrying, or attached to, or own, or are connected with. "The man with the briefcase," "the woman with the camera," "the man with the umbrella," "the woman with the brown dog." Now, for reasons that I can't explain, we just happen to put eyeglasses as being in the second category. Culturally, we think of them as an object that's owned or carried, not a piece of clothing that we are inside. We also talk about "the man with blue eyes," "the woman with long hair," etc. So perhaps eyeglasses seem more "eye-like" than "clothing-like."

I would say "the girl with glasses (on)." There's no reason to say "a pair," since it's obvious.