I would purchase one of those baby carries that strap to ur chest and just pee with him. In that situation I wouldn't be shy to ask a flight attendent or even someone who is sitting close to the bathroom to hold my baby. Its not like they can run off with him...but that's just me! Either I'd pee super fast
If you leave your jacket and only bring baby to the bathroom with you, you can hold baby and pee. I haven't gone on a plane yet, but I had to bring my son into the bathroom with me almost every time for the first few months because I couldn't leave the two kids alone together. Hold the baby with your non dominant hand and get the toilet paper in your hand before you start peeing. It's a pain in the ass, but it works. I couldn't use the baby carriers when I went to the bathroom because even as a newborn his feet would have gotten pissed on. If you can wear baby sideways (like a cradle hold) then that would work and be easier than holding the baby.