What you are describing about your dog is exactly how one of my dogs behaves at the pet store around the rodent cages. Her favorite thing to do there is go from cage to cage, nose plastered to the glass aquarium, tail going a hundred miles an hour just waiting for them to move.
Both of my dogs have high prey drive as that is a trait I specifically look for in a dog as I enjoy the interaction in training that I get with the dog. That being said, my dogs hike off leash and have been taught not to chase wildlife, and the dog that behaves this way at the pet store, does not do this at home with the rabbits
she did in the beginning, however. So even though the dogs have strong prey drives, it can be controlled.
At the pet store we have rules. She is allowed to watch the rodents intently as long as she doesnt use her feet on the glass and does not slam her nose into the glass to scare them into running. If she can stand and watch intently without frightening the animals she is allowed to continue. First aggressive move on her part, and she immediately loses the privilege. I usually have to drag her away before she loses the privilege with her behavior.
Both dogs had quite a bit of training around wildlife, and already knew not to chase, before the rabbits arrived on the scene in the household. I did have to work with both dogs after the rabbits arrived, but training went very quickly since all they really had to learn is that the household animals are the same as those we happen upon in nature. There was a training process though. The dogs did not get free access to the rabbits unless I was there to control the interaction. I worked with each dog individually at first.
Since the first two weeks, both dogs have had free run of the house with the first rabbit when I am home (I had the first rabbit several months before I added the second rabbit). Adding the second rabbit was a piece of cake. Both dogs were like oh, another one of those
whatever. All four run the house together on a regular basis now and have for quite some time. Both rabbits regularly use the dogs as their personal jungle gym, climbing on their heads and everything. If the dogs are lying around and the rabbits suddenly go into 500 mode, both dogs just lay there and watch them with expressions that say what is up with you?
You do need to use common sense. I do not leave the dogs and bunnies loose together ever. If I am going to be out of sight for more than a couple of minutes, the dogs go with me or the bunnies go in the condo. They are still dogs and rabbits who will do doggie and rabbity things. We do live very peacefully together though, high prey drive and all.
The first step in teaching the dog (besides basic obedience) is to teach the dog self control/impulse control. Do a google search for Its Yer Choice and you will find material on how to start this. Then build on that.