I would first like to know whether you are actively trying to kill his character for good or just getting rid of some of his gear.
In the former case, having him falling (either from a building or a plane) would make his armor pretty useless. Making him swim would also force him to let go of his military armor. Without the armor, he's gonna have a bad time. Simply parting him from his arcane arrestor would give mages an edge against him again. The best way to put him down permanently will be with unconventional weaponry (fire/heat, extreme cold, electricity, pressure, poison gas, etc).
If you just want to part him his gear, using sonic weaponry will do wonders, like you found out. Also, like
Tagz noted here, having some routine patrol pull him over should do the trick too.
RHat also noted that his cyberware can be vulnerable, if he's using any.
Here, I would suggest that you trick him into a work, something along these lines:
- Call him for an exclusive job (bodyguard some VIP, for instance)
- Ask him to meet the target in a room (or make him wait in said room for whatever other reason)
- Seal the room and put him to sleep with gas or crank up/down the heat
- Tell him that he'll only live by stripping naked and putting all his stuff in a box
- Special team enters, gets the box and knocks him out
- He awakens with a message: "Next time, I won't be so kind to you -Villain McEvil"
You could put the whole group there just for extra evilish fun.
Then again, more of his backstory would help to brew the exact way to put him back with his char naked. What corps has he run against? What enemies could be well aware of him as a dangerous enemy? Who could be actively hunting him down?