Teleporting boats with @e is messed up.
I was testing with the @e. I teleported different entities while I was riding them, with all but boats, I went with them.
It teleported fine until I got in it. Then it just kind of sunk. I got out it still sunk. After disconnecting from the world it worked.
To reproduce it:
1. Set a command block to teleport an entity.
2. Get in a boat
3. Pull a lever that activates it
4. It doesn't teleport like other entities.
Related issues
is duplicated by
Comments
Same problem in 14w11b. Boat teleported into the ground. But I've activated the command blocks with a golden pressure plate.

Is this still in 14w30c?

Reconfirmed with 14w34d

Is this still an issue in the current Minecraft Snapshot 15w47c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Yes this is still a bug in 1.9 and the latest 1.9.1 pre-releases.
Here's some other things I've noticed with this issue.
Teleporting boats more than 10 blocks away seems to work, but less will not move you or the boat.
Applying a velocity to a boat also does not work, and the boat will not move while a player is in it.
Teleportation DOES work on a boat if it is empty, or if it has a different entity in it, but not a player.
Teleporting minecarts / other rideable entities while riding them works completely fine. It seems this is a boat specific issue, possibly caused by the new boat mechanics / latency code.

It is still an issue in 1.9.2
Still an issue in 1.9.4

Still in 16w21bSummary should be changed to mention boats
Still in 1.10. But: The /tp command works for boats when the x or z coordinates will be changed. Completely vertical teleportation wont work, but incrementing ~1 or ~-1 will work.
Note: It is the exact same issue when a boat goes through an end gateway with a player.
The comment just above me, describing that boats can only be teleported on the x and z axis are still true in the latest snapshot 16w42a. Although I found it would not tolerate any amount of up or down teleportation at all.

Most likely this bug was fixed with before the addition of the new boats (1.9), and then the issue was mixed up with MC-97513
This bug was actually caused by minecraft 1.9 boats, this was not an issue with boats before then, I don't remember why this wasn't a duplicate for the one you listed, but it's usually been treated separate.

If so, why are 1.8.x versions marked as affected?
Also, this ticket says that only boats are affected, which not true (at least not right now)
Well I just tested it in 1.8.9 and boats can be teleported upwards while players are still riding in them, I do not know why they listed 1.8 as an affected version, but to the "only boats are affected" I'm not sure, I didn't submit the glitch I only am saying what I know, if you think that if the other glitch is solved it will solve this then sure, mark this as a duplicate, it's not my area of knowledge.
I tested it, and the problem appears on 1.9. 1.8.9 seems to work correctly. I'm not sure what caused me to say this was a boat specific issue up above, since the problem in 1.9 seems to affect boats, pigs, and horses. It is still true though that it does not affect minecarts. Not sure why it was marked for 1.8.
14w08a Has the original issue described, but the effect is different than the current issue. I believe the original bug was fixed before 1.8, but this new bug was introduced in the 1.9 snapshots, and people jumped on this thread. MC-97513 more accurately describes the current state of this issue.
This is not fixed in the 17w06a snapshot.

@unknown, are you sure that your issue is not MC-97513?

Confirmed for 1.14.4
Confirmed. This bug happens with any entity while the player is riding it.