Unknown tool for making holes in vessel (4)
I believe the answer is:
yawl
'vessel' is the definition.
(yawl is a kind of vessel)
'unknown tool for making holes' is the wordplay.
'unknown' becomes 'y' (algebra).
'tool for making holes' becomes 'awl' (I've seen this before).
'y'+'awl'='YAWL'
'in' is the link.
(Other definitions for yawl that I've seen before include "Sailing vessel with two masts" , "Sailing-ship" , "boat? The reverse" , "Two-masted sailing vessel" , "Ships small boat" .)