Through bolt with counter sunk SS hex bolts using nylon locking nuts or Locktight. I don't have much faith in lock washers and I avoid carriage bolts because they spin when the wood starts to rot especially if you are trying to loosen a Locktighted nut. Since I am always replacing bunks because they are rotten, carriage bolts always spin in my experience.
Another school of thought is to continue to use the galvanized lag bolts so that they rust out at about the same rate as the bunks rot out. Just replace everything at once every 5 years or so. The first loose lag bolt is a sign that you need to buy materials.