You could also consider putting the rabbit cage up on some kind of table. I understand that that is really not an ideal situation for a rabbit, but it might be the best you can do right now.
I dont know what type of cage you have, but if you got the giant super pet cage you could stick it on an end table. Obviously this wont work if you have an NIC cage.
This might not be possible depending on how big your rabbit is and how accustomed it is to its regular home. I have a mini breed, so this is what I might do.
Actually, I would think about the type of cage you have regardless. I had to put Lulu in a "real cage" because I was worried if some freak thing was to happen with one of the dogs they could break though an NIC cage. I would make sure it was super sturdy, even after the animals become friends.
I really think that most puppies will just ignore the rabbit or maybe try to play with it. Either way I doubt it has the hunting instincts yet. I would start introducing them REALLY soon though. If the dog grows up knowing the rabbit is not food you wont have a problem later. Training an older dog could be much harder.