At sea stop son boarding a vessel (5)
I believe the answer is:
avast
'at sea stop' is the definition.
(nautical term for 'stop')
'son boarding a vessel' is the wordplay.
'son' becomes 's'.
'boarding' is an insertion indicator.
'vessel' becomes 'vat' (vat is a kind of vessel).
'a'+'vat'='avat'
's' put inside 'avat' is 'AVAST'.
(Other definitions for avast that I've seen before include "Stop, nautically speaking" , "Stop on board" , "Stop at sea" , "Hold fast! (naut.)" , "shout stopping the ship" .)