Place beans in large bowl. Add enough water to cover by 3 inches. Let stand overnight. Drain beans; set aside.
Preheat oven to 350°F. Cook bacon in heavy large pot until crisp, about 8 minutes. Add onions and saute until translucent. Add beans and all remaining ingredients to pot. Bring to boil.
Transfer pot to oven. Bake uncovered until beans are tender and liquid thickens, stirring occasionally, about 4 hours.
Notes
This recipe can be made 1 day ahead. Cover and chill. Bring beans to simmer before serving.