The Flower Garden Banks are amazing. Folks just don't understand how special they are until they get there. Unfortunately there is only one boat going out there now, The Fling. It is based from Freeport. The boat has not been well maintained and it is a dump. Twenty years ago, there were three boats going out there.
I don't know who, but I have heard there is someone running day trips to Stetson Bank from Galveston. A simple internet search should reveal this.