Soak the beans, either overnight or by the quick soak method: cover with water, bring to a boil, cover, turn the stove off, and let the beans sit in the hot water for an hour or so. Then drain and use.
Put the beans, onion and ham in a large stockpot. Cover with water by 1 1/2" . Bring to a boil, then reduce the heat to a simmer, cover partially and simmer 2 hours or so, until the beans are tender. Watch the water level and add a bit more if needed. Taste and add salt and pepper as desired.