The most common and most likely answer to this crossword clue is the 4 letter word YAWL
I've seen this crossword clue in The Daily Telegraph
Y
A
W
L
Buddy explains!

The straight part
We know that "Boat" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case boat = yawl.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does YAWL mean?
YAWL noun- A small ship's boat, usually rowed by four or six oars.
- A fore-and-aft rigged sailing vessel with two masts, main and mizzen, the mizzen stepped abaft the rudder post.
- To cry out; to howl.