Are they both neutered and for how long? If they aren't neutered, then yes separate until neutered. Then 4-8 weeks post neuter you will need to go through the bonding process.
If they are neutered, you could try distracting the behavior with feeding time, or pushing him off after a few seconds. If he doesn't take the hint, then I would probably separate to give the other bunny a break. Then when both have settled down, attempt to put them back together. There will probably be a little mounting once back together, but if it continues for more than a few minutes, you may need to consider separating for longer(hours to days) until they've had a chance to adjust to their new home, then try putting them back together. The risk with this though, is that separating can sometimes risk affecting the bond, and rebonding may then become necessary.
It isn't uncommon for changes and new territory to spark this sort of dominance behavior in spayed/neutered rabbit groups, but usually it settles down fairly quickly. It's when it doesn't that temporary separation sometimes is needed, because continued humping can sometimes cause the other rabbit to become agitated if it goes on for too long.