I'm currently doing this quest. and am at Help Yennefer Find the Djinn. We boarded the boat and now are stuck because the boat is parked on top of another boat. How can I get the boat moving?

So you sit in front of her in the boat and the boat isn't moving because it is on top of another boat? Try to reload an older savegame and hope the boat isn't on top of another boat this time. If this doesn't help patch the game to latest version (if you haven't done this already) and see if this thil fix the problem.

I closed the game, did a verify/repair and restarted the game. I loaded a save before I talked to Yennefer then went down to the dock where I saw only 1 boat. When I went back to the dock with Yennefer the second boat was there.

I went back again and sailed the boat in the harbor to a different location. When I continued the quest, it generated the second boat. All is well now.