Both neutered? I would start with neutering to get all hormones out of the situation as that will likely help your rabbit out
Rabbits are prey animals and canines are often the ones hunting little buns aside from larger birds. Your rabbits instincts have likely kicked in and he is acting on fear of this new creature in his home. Keep introducing the way that you are (pup in his crate and the bunny out) and monitor to see if they both start to feel comfortable after a while. It may take weeks, months, or even years. Since your rabbit was there first, you have to let your bunny set the pace with bonding. If at any point you feel there is no chance of them getting along, the rabbit is going to need its own area where the dog is not allowed and visa versa. If your rabbit previously had full access to all of your house, downgrading him to one room might stress him out for a little while because he wont know why hes being limited to such a smaller space