If your hypothetical japanese person thought that a living object made a noise, and wanted to express concern over the fact:
If your hypothetical japanese person thought that a non-living object made a noise, he would not say そこなにがある？ and he probably wouldn't even say そこになにかある？ because neither of those sentiments make any sense. You can set aside the japanese and consider whether our average human being would even think to ask the question "What is over there?" in response to a noise.
A hypothetical average japanese person would just say something along the lines of その音なに？ and be on with it.
Your scenario is pointless. If you want to know more about ある vs いる then ask about that, don't get pointlessly hypothetical about language. It's something that only exists in practice.
If we boil your question down to "is ある or いる preferred when you have positively no clue who or what the subject is" then the answer is neither. You'd say something that doesn't involve ある or いる, because in that case you don't have a reason to use either of them to begin with.