Place carrots in a steamer over 1 inch of boiling water, and cover. Cook until tender but still firm, about 6-10 minutes. Drain. Meanwhile, in a small bowl combine crushed crackers with 1 tablespoon melted margarine. Mix well and set aside.
In a medium skillet over low heat, heat the remaining 2 tablespoons of margarine and saute onions until tender. Stir in flour, salt and pepper. Cook for a few minutes, stirring to prevent browning. Gradually pour in milk, stirring constantly. Increase heat to medium and cook until bubbly and thickened. Add cheese and stir until smooth. Fold in carrots.
Pour mixture into a 9x12 inch baking dish and sprinkle with the crumb mixture.
Bake in preheated oven for 20 minutes, or until bubbly and golden brown.