Actually, I was rather thinking of the late Knights Templar, after Jerusalem had fallen. They had quite the armed merchant fleet (which seems to have disappeared when they went down) and there are a lot of other items of theirs that went 'missing'. There are rumors of involvment with various magics and some claim that Freemasonry has its origins in the Templars. In any case, some of the theories about them would lend them as a basis for your Templars (or perhaps it's the other way around and the Knights Templar were a group who became too public and got caught out by their enemies). In any case, it's developing into an interesting and original story.
Author's response
Thank you for the information. I look more into it, the sources I read didn't tell me much other than the fact that the Pope disbanded them after the king pressured him to. I'll look a lot more thoroughly now.