Since i couldn't quite figure out Instruments or Shark, and my project is so small right now, I started just taking out lines until something made a difference. In my custom EAGLViewController, in my viewDidLoad method, I had this line:

self.view.backgroundColor = [UIColor colorWithRed:0 green:0 blue:0 alpha:1];

Where self.view is the EAGLView itself. Apparently this was my problem. Once I took it out, the whole thing started running faster. Not entirely sure why, but then I'm not entirely sure why I had that line in there to begin with.

Edit: Looks like I spoke too soon. This helped, but did not solve the entire problem. Back to trying to figure out Instruments/Shark.