There are a few options that come to mind (and I did a bit of googling).
You can get armor piercing concussive guns; obviously non-lethal.
There's also a very rare drop called Fiasco's Facebreaker that is essentially an armor piercing concussion hammer.
An alternative way to deal with it (although much harder to pull off, this doesn't require rare/unique items) could involve glitch traps. All you have to do is lure them (or use a swapper) into a glitch trap that is aimed outside of the ship. This should knock them out. Then you have to quickly bring your pod over and pick them up before they die in space. I'm pretty sure this will work. I've personally only tried it ~2 times and failed at getting the pod to them both times though; so no promises.
As confirmed by Studoku in comments, throwing them into space works. He used broken windows; which is even better because it doesn't require anything specific.