In a 5-quart saucepot, mix soy sauce, rice wine vinegar, onion, brown sugar, lime juice, ginger, garlic, bay leaves, and pepper. Add chicken thighs. Cover; heat to simmering on high. Reduce heat; simmer 1 hour.
Serve with long-grain brown rice (cooked as label directs, with ginger, bay leaf, salt, and pepper) and green beans (steamed with garlic and lime juice).