It is pretty rare for a gun to be off 3 mph and pretty common for someone to believe a gun was off 3 mph. It can happen but it is pretty rare. If one gun is reading slower than other guns at a given location then you might be fairly certain it is reading low. Of course you'd use the other readings in that case.
Velocity vs Control vs Movement - Each pitcher has to determine what combination of the 3 he can achieve and work hard to reach that goal. At some point every pitcher is going to plateau on velocity and then it is certainly time to focus more on control and movement.
There might be some guidelines that most college coaches follow relative to velocity but if a pitcher has exceptional movement and/or control the "required" velocity number is going to drop a bit.
I would tend to agree that a college pitcher who can consistently work 87-88 with command and some off speed offerings is going to be able to pitch in pretty much any college league. The pitchers in the recent UCLA v. USC game were mostly throwing about 87-89 and touching 90.
Judy,
It doesn't sound to me like your son had a particularly poor outing. Wait and see what happens over the next few games before worrying about it.
IMO, you might want to start by asking his current pitching instructor about the possibility of setting up a long toss program for him to do. Be aware that if he's throwing pens at school, pitching in games and throwing pens for the pitching instructor then he's not going to have much opportunity to long toss.