Optimo is considered one of the top "custom" hatters....they did a bunch of hats for films like Road to Perdition, and Public Enemies (including Johnny Depp's BEAUTIFUL ox blood fedora from that movie). But they'll cost ya.
But I've got to give another shout out to John Penman of Penman hats. He's going to be making me a hat similar to the Public Enemies hat (just not in the glorious ox blood, you've got to go to Optimo for that). He has his own line of hat designs or can do any Indy hat you want. But he customizes the specs of the hat to fit your head and face shape. Plus, it's all hand made.
Art Fawcett of Vintage Silhouettes also does custom hats. No personal experience, but have heard nothing but good things about his work.
Borsalino, akubra, porkpie hats, henschel, greek fisherman hats, kangol, stetson hats <-- these guys are local to me, but they do internet business as well.....I've found them to be quite helpful...picked up a Stetson from them not too long ago.