We then got into a fight about how she felt I was snooping on her
You express anxiety and pain over concerns you have and her reaction is...
A. Being empathetic and loving in her words to you
B. Putting your mind at ease through action (coming home ASAP)
C. Berating you for learning that she is up until 4AM with him
She chose C. It's not only unloving and disrespectful, but it is a continuation of manipulative/controlling behavior on her part.
he even called me to talk. I honestly think he's telling the truth
Oh no.
When I discovered on my cell phone bill that my wife and BFF (a neighbor, father of my kid's friends, husband of my wife's BFF and the family we spent significant time with) had increased their texting to each other to thousands per month over a few months, I sat down and talked with my BFF. Face to face. He looked me in the eyes and told a story of how it wasn't what it appeared to be. I walked away believing that he was telling the truth -- that the quantity just reflected a good friendship, that there was nothing there, that their banter was innocent but the quantity just got carried away, that they'd cut back because they didn't want to cause worry, etc.
What ended up happening was...
1. They knew how they had been caught and figured out other ways of communicating
2. The affair went underground and intensified
3. They successful hid things for 3 more months until my BFF's wife caught them
Back to your situation. Go back to what you KNOW...
1. Their texting/Skype quantity was out of hand
2. Their timing of communication showed a deep level of commitment to each other
3. Your wife's treatment of you corresponded to her time with him (both when she was/wasn't Skyping/texting and when she went no contact with you for her visit)
You KNOW that, at a minimum, their relationship was inappropriate and a full EA.
she's doing some thinking, as am I.
Your only conclusion should be that your wife has been having an EA with her uncle. Even her uncle threw some blame her way indicating that if anyone had feelings it was her. While I don't think that is the whole truth and is a manipulative/gaslighting tactic on his part, it does underscore that your wife is fully at fault here. Her actions have been WAY out of line, she needs to own up to that and she needs to go full NC (no contact) with her uncle if she wants to save the marriage.
The result of her thinking better be right along that line -- that it was inappropriate, that it was an EA, that it was unloving/disrespectful to you and that she needs to take immediate steps to fix things. That means, for starters, she cuts short her visit (or, at an absolute minimum, the uncle goes home NOW) and her uncle does not come to visit at your house. When she gets home, she is fully honest (i.e. seeing ALL of her texts and not finding gaps in them would be a good start), she is transparent (you get access to everything, there is no deleting and no apps that allow hidden communication show up in the coming days/weeks) and then she seeks out help for herself (i.e. an individual counselor).
Given what you've written about her so far, I'm betting that you'll get something different. She and your uncle will realize that they've been caught through phone records and the eyes around them during the visit. They'll come up with a storyline to minimize/excuse their closeness and, very possibly, to make you look jealous, manipulative, controlling and paranoid. Something along the lines of "my husband and I haven't been getting along so well because he is _______ and my uncle has been a confidant and help in encouraging me to find ways to fix our marriage" would be a common tactic. They'll also sort out ways to hide their communication -- anything like WhatsApp, Facebook Messenger, etc. can serve the purpose or, at a more advanced level , she could get a burner phone. Then they will be on their best behavior when they are around your mom or anyone else and will find ways to withdraw away from others to get time alone. They may even try to press forward with his visit to your house. Once they are apart again, your wife will make sure that communications you can detect are limited or even non-existent.
Don't accept anything less than the love and respect you deserve. Don't allow her to make excuses. Don't tolerate her trying to twist the story into "You're snooping" or "You are being controlling". Don't let her shift blame with anything like "Our marriage sucks because you _______, so I went elsewhere for attention. It's ultimately your fault." And certainly don't accept her "thinking" all the way into the weekend while her uncle continues to be there (or even extending into next week with him visiting you). She needs to she the seriousness of what she has done quickly as any other move is just a manipulation on her part to extend the affair.