Both are really good schools. I went to Comair, now DCA, and I was trained well, and I think I got my money's worth. FSI also has a good reputation, but I've never been to the General Aviation side of their training. I did a lot of 727 stuff with Boeing/Flight Safety in Miami, and I thought it was pretty good.
If you don't give it your 100% effort, it doesn't matter which school you go to, because it will be an expensive drain which won't leave you happy. However, if you really bust your backside, and soar, you will do fine at either one of these.
Comair(yeah, I know, DCA) would be my first choice, simply because I went there, and I know it's good and solid. But if for some reason you chose to go with FSI, it's a good choice, too. Some people like a Ford, some like a Chevy........I like Dodge.