My ex and I used to do the same thing until one day I called and there was another guy in her bed. With a second girl. And nothing innocent was going on.
Anyway,
After many years of sleep-skyping, I've found that boom microphones don't work as well as you think.
In-line microphones may work better when they're hanging off the side of the pillow. Standard Apple and Samsung headphones should still pick up your breathing. You might also want to try slipping heat shrink over the cable to give the cable the stiffness of a boom mounted mic to reduce movement noises.
I'd just like to mention that the solution to this problem will be very specific to your sleeping patterns - if you move around a lot in your sleep, if you snore loudly, if you sleep in the middle or one side of the bed etc. I sleep like the dead - absolutely still until morning, which means i never actually have to put in effort into making my bed. It also means that my microphone stays put the entire night. If you move a ton, wireless headphones may be the way to go. Something like the Nokia BH-503 would be perfect in that situation, especially with the microphone in place just in front of the ear. It should be able to pick up the sound of your breathing. A larynx microphone like the Pro-Idee RoadRunner should also be able to pick up other sounds from your throat (including breathing) which can make it feel like you're closer to her. I know it sounds weird but all these little sounds can be really comforting to her and create the illusion that you're right there with her. Of course, only she would benefit though. That's a bit of an outlandish option and I've never used one before so I'd do more research. I've been pretty comfortable with standard Apple and Samsung headphones - the ones that come with their smartphones.
In the meanwhile, if I were you I'd experiment with sticking something like two big balls of blu-tack to either side of an inline mic to stop it from rubbing against anything when you move. Two cardboard discs might also work. Basically make a cage for the mic to sit inside so it doesn't rub against anything when you move.
I hope I've been helpful