Melt the butter in a saucepan over medium heat and stir in the flour, salt, and pepper. Cook the mixture until it turns a slight tan color, about 1 minute; whisk in the milk. Bring to a simmer, whisking constantly, and cook until thickened, about 2 minutes. Stir in the cheeses until melted and the sauce is thick and smooth. Transfer the Brussels sprouts into the sauce, stirring to coat. In a small bowl, combine cracker crumbs and melted butter. Mix well to coat.