The proper way to do it is with a lathe, which means the barrel needs to be removed to chuck it up and get it centered. If you are threading for a suppressor, take it or send it to ADCO. The threads need to be perfectly concentric to the bore for a suppressor.
If you are just threading for a muzzle brake or flash surpressor, you will have a little more 'tolerance' for threads that are not perfectly concentric to the bore. In this case, you can often get by with using a die kit to manually cut the threads without removing the barrel. Most shops with a capable gun smith can do this. It's also an easy DIY if you have patience and some mechanical ability. The problem is the tools will cost you as much as paying someone!