Unfortunately, the Ender Dragon can no longer be put in a boat as of Minecraft Snapshot 15w49a.
The glitch that allowed players to trap the Ender Dragon in a boat surfaced from Minecraft Snapshots 15w41a to 15w47c (1.9 Minecraft Snapshots). It allowed the dragon to enter the boat if it was placed on the very top of the bedrock pillar, which the dragon swoops down on.
Although trapping the formidable dragon in boats has been discontinued for some time, there have been other successful attempts to find ways to trap the Ender Dragon.
Disclaimer: These methods have not been tested in each version of Minecraft that’s been released since. There is a possibility that readers might be unable to recreate these methods of trapping the dragon in newer versions of the game.
Command Block trapping the Ender Dragon
However, his dragon wasn’t the final boss found in the end. Instead, it was one spawned into the overworld through server cheats and commands. But the mechanics of keeping this dragon in its bedrock cage are the same. They described the process in a Reddit thread here, saying:
“It’s nowhere near perfect, nor was it planned out, but it was pretty cool. I thought it would be nice to post our findings and get feedback from this subreddit community.”
“First and foremost, the cage and system. As we know, you can’t really trap an Ender Dragon. It goes through everything and destroys nearly everything. However, we recently discovered the use of Command Blocks.”
“Now, my roommate found out how to get command blocks and we researched commands. Disappointed that you cannot nest commands within a single block, we created an “if-then” logic circuit.”
“It begins with an active clock. This clock frequently checks for the Ender Dragon. If it returns true the second clock is active, checking in a much, much, much shorter interval. Two command blocks are checked simultaneously. One makes sure that the Ender Dragon is in its cage, and upon failure brings it back.* The second checks for an Ender Crystal that we had to encase in bedrock.”
“The end result was a caged Ender Dragon. We even tossed in a Wither to chase it around because, well, why not? The system allows for you to roam around as you wish without worrying if the Ender Dragon will escape. However, you have to watch out for random shots from the Wither!”
“I should note that our clock system is very compact. I tried to reduce the size in order to reduce the time it takes to perform these checks as well as allow room for more checks in case we try to expand the concept. We want to have a system check for holes in the base of the cage in case someone kills it by hand (because my roommate is a TNT-cannon psychopath) or if the Wither(s) somehow kill it while we’re away from the server.”
“The cage itself was made on a whim and not at all calculated. Somehow it worked out for there being 3-block-high holes so the Wither cannot escape but it doesn’t do well with keeping the dragon in the center. Our teleport system puts him more towards the front of the cage. I’m sure that someone who likes to perfect design and execution will find a way to calculate it all. . . but we don’t care. It’s pretty sweet, as it is.”
“Commands can be found in the album, as well as a monument to the reason why I have to oversee the activity of my roommates.“