In slow cooker, combine onions, garlic, tomatoes, molasses, vinegar, brown sugar, chili powder, salt and pepper. Top with pork.
Cover and cook on low until pork is tender, 6 to 8 hours.
Remove pork to platter; tent with foil to keep warm. Whisk flour with ¼ cup water until smooth; whisk into slow cooker.
Cook, covered, on high until thickened slightly, about 30 minutes.
Separate pork into portions and serve with sauce.
