Very tiny boat with a man in charge (9)
I believe the answer is:
subatomic
'very tiny' is the definition.
'boat with a man in charge' is the wordplay.
'boat with' becomes 'sub' (I've seen this before. I am not sure about the 'with' bit.**).
'man' becomes 'tom'.
'in charge' becomes 'ic'.
'sub'+'a'+'tom'+'ic'='SUBATOMIC'
(Other definitions for subatomic that I've seen before include "Like 9 across" , "Smaller than a basic particle of matter" , "Of smaller than elementary particles" .)