Combine 1/2 cup molasses, 1/4 cup mustard, and 3 tablespoons vinegar, stirring well.
Place salmon and onion in a shallow dish.
Pour molasses mixture over salmon and onion. Cover and marinate in refrigerator 8 hours, turning occasionally.
Remove salmon and onion from marinade, reserving marinade.
Place marinade in a small saucepan. Bring to a boil; cook 1 minute. Coat grill rack with cooking spray; place on grill over medium-hot coals (350 to 400).
Place salmon and onion on rack; grill, covered, 4 minutes on each side, or until fish flakes easily when tested with a fork and onion is tender, basting often with reserved marinade.