I hadn't thought of the boat being the Perfumed Seneschal! Great catch! I already had the feeling it couldn't be Reznak (who Dany thinks) or Varys (who the reader is bound to think), so this third option makes sense. I think it's warning her for all the people on that boat, Tyrion, Jorah ánd Moqorro. (Penny is also on the boat, but I don't see how she could be dangerous.)
@SaltThroneHeir You said ' IMO, it seems pretty obvious that Tyrion wants the good for Dany.' Why is that? In my opinion Tyrion doesn't have Dany's best interest in mind (at least in the books), and is motivated by his own desire for vengeance and power.