Trust your baby! He is still feeling badly- could definitely be from teething. His ears may hurt from that, too. Try giving him extra yummy stuff. Maybe a yogurt drink (Yobaby banana is my son's favorite!) or a smoothie that you make with bananas, plain yogurt, and frozen blueberries and/or raspberries. You can also try something he can really gnaw on- like a hard breadstick (keep an eye on him though) or a gerber teething biscuit.
He'll come back around. It's great that he's still nursing, and you may want to give him a bottle of breast milk as well. I found that my son really liked chewing on the nipple when a tooth was coming in!