There are lots of fin companies out there, but most will not make fins/'new designs' for random people. Some will for a nominal fee. Rainbow use to make some good fiberglass wake fins, but they discontinued the line. Futures will make cut custom fins on their CNC (you will need to generate a CAD file) but they fit futures boxes (and it will be a $400 cutting fee). There are dozens more.
The easiest and most practical thing to do to start out is look at some cheap plastic or aluminum fins that are already drilled for your board template. Then you can grind and shape to what you want. Look at the site Mitch suggested, they are cheap black plastic and easy to reshape.