Agree with dhays. Your AC system pulls interior air from throughout the boat, re-cooling it and blowing back into the cabin. The fumes are likely being pulled up from below deck when the unit(s) are running. When off, the fumes stay low.
It would not take much fuel - diesel has a pretty strong odor - but this should certainly be corrected.
I suppose it's possible that you could have someone turn on your bilge blower and see if you smell the same thing wherever that air exits.
Don't know the age of your boat so a leak could be at a fuel fill line, a fuel tank, etc. etc. Unless there's a diesel-y rag laying around.