I have no idea if you need to do anything special to ship animals in or out of Puerto Rico, but I would call Fish and Wildlife in PR and then the one in Florida and find out what the process is. They'll know exactly what you need to do and tell you how to do it. I had to speak to the F&W here in Florida to figure out how to send him his Colombian boa to El Salvador and the process was actually pretty simple, it was just going to take several months to get the permit.
I don't know if it's easier and faster from PR to the US, but it didn't seem complicated, just a little slow.
And perhaps you don't need to do anything special at all, I just don't know.