Many people who had their ears pierced as a kid or went to the mall, have most likely seen the piercing gun. But for piercings done at tattoo shops and done at home are usually done with a needle. Surprisingly, the needle at home are probably better then the gun.
One main argument against the gun is that it cannot be autoclaved, a sterilizing machine for needles. The gun, which is normally made with plastic, can only be wiped clean with a disinfectant after each piercing. But that is not as thorough at cleaning as the autoclave machine.
Another argument against the gun is that the people that use it have not been very well trained beforehand, some say they only went through two weeks of training on teddy bears and barely got to use the gun themselves. A professional body piercer has a training program that can take a few years not a few weeks.
The gun, while possibly infected, and used by poorly trained people, is a lot cheaper to pierced by, usually just a few dollars with the jewelry included. A needle piercing will be almost twice as much. Also, the gun will not look as scary to some people, such as young children getting their first piercing, as a needle would. The more scared they get the more pain they will think they are in. The gun would be best used on small children and people with low pain tolerance.