The most common and most likely answer to this crossword clue is the 3 letter word ARK
I've seen this crossword clue in Independent
A
R
K
More clues leading to the result ARK
- Out of hospital, listen to chest
- Sacred box that housed survivors
- Get a load of that missing heroin in old vessel
- Old vessel, unlit, heading off
- Leaders to appoint Roula Khalaf as a response to climate change?
- Old pairs’ refuge left high and dry
- Boat mischief, line being cut
- At work, prime cut of animals saved in this
- Vessel built in Samarkand
- Box ’ear
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 = ark.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 ARK mean?
ARK noun- A large box with a flat lid.
- Noah's Ark: the ship built by Noah to save his family and a collection of animals from the deluge.
- Something affording protection; safety, shelter, refuge
- A spacious type of boat with a flat bottom.
- The Ark of the Covenant.
- A decorated cabinet at the front of a synagogue, in which Torah scrolls are kept.