Ferry is inexpensive, but takes a whole lot longer than flying. And non-residents can get bumped. So we fly, and we use Vieques Air Link.
VAL will get you there safely and quickly. No airline gives you loads of room or luxury when you're island hopping.
I really wish their weight limit were the same as other airlines (35lbs. for VAL, 50lbs. for major carriers from the states); we've gotten hit hard ($$) for being overweight. Annoying as hell. Women's purses and any carry-ons are weighed and added to your weight total. Not that you need a big wardrobe in Vieques, but I'm a diver and my wife is a snorkeler. Masks, snorkels fins, camera and regulator add up quickly.
Planes are small and loud - earplugs a very good idea.
Fares are better than competitors, but higher than they should be, in my opinion (approx. $150 pp round trip from Isla Grande to Vieques; higher from SJU to Vieques).
But VAL runs pretty much on time, weather permitting, and they get you to Vieques or Culebra* and back quickly and safely. And the airline isn't the reason you're going anyway, right?
*They also fly out of Ceiba, the former Roosevelt Roads Naval Base