I was an intern at SkyWest back in '05. They've got to be one of the nicest bunch of folks (relatively speaking) around. But i've got a buddy at Chataqua in BUF and he says that its one of the places that you would be proud to work at. I think either would be a fine choice, i'll soon be having to make that exact same decision.
of course both companies have their negativity. As far as bases go, i'm piedmont so i couldn't comment on that.