I'm afraid I am not an expert on training dogs; you may need to have your dog attend training classes so he'll actually follow your commands to stop, but here is a link to the House Rabbit society regarding interaction between rabbit and dogs.
For now, until you can train your dog to stop barking at your bunny, can you keep them completely separate to prevent your bunny from going into shock if it gets too scared?
Some dogs do fine with rabbits, even hang out with them with no problem (supervised of course), while others really are a danger to the rabbit no matter what. Once he's been through some sort of training by you or a professional, you'll really be able to determine that.
Keep us updated! Let us know how it goes.
Does anyone else have other pets, cats, dogs etc that do or don't get along with your bunny?