In a large bowl, combine soy sauce, vinegar, garlic, and black peppercorns. Add chicken thighs and coat evenly. Allow to marinate for at least 20 minutes, or overnight for deeper flavor.
Heat oil in a large skillet over medium heat. Add onions and sauté until translucent. Remove chicken from marinade (reserve the marinade) and add to the skillet. Cook until each side is golden brown, about 3 minutes per side.
Pour the reserved marinade and water into the skillet. Add sugar and bay leaves. Bring to a boil, then reduce heat to low and cover. Simmer for 25 minutes, or until chicken is cooked through and tender.
Remove the bay leaves. Increase heat to medium-high and cook uncovered for about 5 minutes, allowing the sauce to reduce slightly. Serve hot.