Increased velocity will come through improving your mechanics, getting stronger and growing. You have no control over the latter.
Getting stronger will be best accomplished by a baseball oriented strength training program. Perhaps the best way to do this would be to find a good strength training facility that has a program designed around baseball. Once you have trained there for a while, you can probably then proceed on your own by following the regimen you were taught.
Be sure to keep your protein intake up since you are working out hard. You don't need supplements, just eat lots of protein containing foods.
Keep the rotator cuff balanced by doing the Jobe elastic band exercises. This is very important.
Improving your mechanics will probably require working with a good coach. Even throwing (as opposed to pitching) mechanics often have room for improvement.
Try to make sure that whenever possible, you set well before throwing. A stronger base makes for a stronger throw.
Running and agility training will help as well. The agility training should help a great a deal toward faster footwork, which in turn will decrease release time. Yankee's point on transfer is also well taken.
This will take time. Work hard, but don't rush it.
