Rinse the dry navy beans under cold water and pick through them to remove any debris or discolored beans. Place the cleaned beans in a large pot and cover with water by at least 2 inches. Let them soak for 8-12 hours (or overnight) to soften and reduce cooking time. This soaking step is essential because it helps the beans cook evenly and reduces the gas-producing compounds that can cause digestive discomfort.
Drain and rinse the soaked beans thoroughly. Place them in a large pot, cover with fresh water, and bring to a boil over high heat. Once boiling, reduce the heat and simmer for 45 minutes until the beans are partially cooked but still firm (they should not be fully tender yet). This parboiling step removes excess starch and ensures the beans will have the right texture when finished cooking with the sauce. Drain and rinse the beans again before proceeding.
While the beans are parboiling, dice the onion into 1/4-inch pieces. In a small bowl, whisk together the maple syrup, brown sugar, molasses, tomato paste, mustard powder, salt, black pepper, smoked paprika, and apple cider vinegar until well combined and smooth. I like to make this flavor mixture in advance because it ensures the spices are evenly distributed and won't create clumps when added to the beans.
Transfer the parboiled beans from Step 2 to a slow cooker or heavy-bottomed pot. Add the diced onion and the flavor mixture from Step 3, then add 3 cups of water and stir well to combine. Cook on low in the slow cooker for 6-8 hours, or if using a stovetop pot, bring to a gentle simmer and cook for about 4 hours, stirring occasionally. The beans should become very tender and the sauce should thicken slightly. If the beans seem dry at any point, add a bit more water to keep them submerged.
If you prefer a more concentrated, caramelized flavor and a slightly thicker sauce, transfer the cooked beans to an oven-safe baking dish (9x13 inch or similar) and bake uncovered at 325°F for about 30 minutes. This step is optional but adds depth and allows some of the liquid to reduce, intensifying the maple and molasses flavors. Watch for the edges of the beans to slightly darken—this creates wonderful flavor complexity.