Heat oven to 350 degrees. Grease a deep 1½-quart casserole dish with nonstick cooking spray.
In a small bowl, whisk together the milk, egg whites and flour. Pour the mixture into the prepared baking dish. Split open the chiles and rinse under cold running water to remove the seeds; drain on a paper towel.
In a small bowl, combine the cheeses; set aside ½ cup of the cheeses for the topping.
Alternate layering the chilies and cheese in the baking dish, submerging them in the egg mixture. Pour the tomato sauce over the top and sprinkle with the reserved cheese.
Bake for 1 hour or until the center is set and the egg batter is puffed all around.