Really a shame about Stewart. That's a terrific little airport, and one would think Independence could have done pretty well there.
One problem Indy has is that you can't book it via IBM's online travel reservation system due to a technical problem between Indy's system and Galileo, from what I've heard. So the IBM travelers to/from that airport -- and there are lots, because of some big IBM plants at Poughkeepsie and East Fishkill -- have to jump through hoops to book Indy. Which means many of them don't.

That alone could have made the difference.
Stewart has taken a couple blows lately. Southeast also served Stewart.