Turn slow cooker on high to preheat. Drain beans and pour them into large Dutch oven along with 8 cups water, baking soda, and bay leaves. Bring to boil over medium-high heat, and use a slotted spoon to skim the foam off of the top. Boil 15 minutes.
While beans cook, chop bacon into 2-inch pieces, and in a large non-stick skillet sauté bacon and onion over medium-high heat until fat is rendered from bacon and edges of onion begin to brown slightly about 7-8 minutes. Place bacon and onion in the slow cooker. Stir in 1/3 cup molasses, brown sugar, and boiling water.
Once beans are done boiling, drain beans and transfer to the slow cooker, discarding bay leaves. Give everything a good stir and place aluminum foil directly on the surface of beans, then cover slow cooker with lid. Set slow cooker to LOW and cook until beans are creamy and tender 10-12 hours.
Turn off slow cooker and remove the lid and discard aluminum foil. Stir in the remaining 2 tablespoons molasses, maple syrup (optional), mustard, and vinegar. Season with salt and pepper to taste. Cover slow cooker lid and let beans sit until the sauce has slightly thickened about 15-20 minutes. Serve.