"Which is better?" is subjective. Are you trying for a literary prose, or to make the most amount of sense?
If, to make the most amount of sense, one would say:
Upon looking, he couldn't tell where the sound came from, but he knew it wasn't the wind.
To keep your similar sentence structure you could use glance and simplify:
At first glance, he couldn't see the cause of the sound he had heard, but he could swear that it wasn't the wind.
If trying to be artistic in your prose (while keeping the structure similar), one could say:
At first glance, he* couldn't suss the root of the noise he had heard, but (he) could swear that it wasn't made by the wind.
and the point would be more clear than your original sentence. Keeping or leaving out the last he in the sentence doesn't change the meaning.
*Some might say it would be best to use a name here instead of the first pronoun in literary prose.
In English, it is an awkward way of speech to try and find out what kind (sort) of noise was made. All noise and sound comes from a source and we infer the 'kind' by the source. The sound from an elephant is an elephant sound, but to say it was an elephant 'kind' of sound w/o knowing the source is the same as saying the unknown source made a sound like an elephant. So, in this instance, it is better to say he couldn't find the source of the sound, than it is for him to try and sort out what kind of sound he had heard.