Preheat oven to 325 degrees.
Place beans in a large pot and add enough water to cover; let soak overnight.
Drain and return to pot; add enough water to cover and simmer over medium-high heat for 30 minutes.
Drain and transfer to a large bowl; stir in molasses, maple syrup, mustard, and tomatoes. Set aside.
Coat the bottom of a Dutch oven or a 9-by-13-inch high-sided baking dish with olive oil.
Add onions and top with bean mixture.
Add enough boiling water to cover bean mixture by 1 inch.
Cover Dutch oven with lid or baking dish with parchment paper-lined aluminum foil.
Transfer to oven and bake until beans are softened, about 1 ½ hours, checking water level and adding more as necessary.
Uncover beans and continue baking until thick and syrupy, about 45 minutes more.
Season with salt and pepper and serve.
