First, this is just a personal opinion, not a researched fact from the command:
1. Paint balls will crush at depth, plus the gelatin would disolve in the water. So strike that. Plus they'd travel about a foot and a half...maybe
2. Best option 1: Lazer tag. Would have problems in turbid water though.
3. Option 2: A gun that fires small "toypedo" style projectiles. water pressure and cavitation will keep anything from traveling very far/well, so you need something that will corkscrew through the water like those toys.
4. Option 3: As mentioned, some kind of blunt tip for a spear gun, however its flight characteristics will be impacted by the need to make it blunt enough that it doesn't harm the diver....
Just my two cents.
May I present Baldar Blunts - This is something a few of us ScubaBoarders with another backround in history (Society for Creative Anachronism, Inc.) know about and some even experienced either shooting (me!) or getting hit (many people, JustJoe even!)!
For kicks, I've tried dinking with a ball in the water. You need considerable pressure and rifling to get the round little ball do anything.