Drain the beans, cover with fresh water and bring to a boil. Simmer for about 1 hour.
Drain and rinse the beans, then transfer them to a slow cooker insert. Add the tomato puree, brown sugar, molasses, dry mustard, bacon, onion and 1 1/2 cups water and stir to combine. Cook on low until the sauce is thick and syrupy, 8 to 10 hours.
Before serving, stir in the cider vinegar and season to taste with salt.