It depends. If the 'something' is a pronoun. we can only 'wipe it/them out', not 'wipe out it/them'.
If the 'something' is not a pronoun, then the longer it is, the more likely it is that 'out' will precede it:
1. Humans have wiped the species out / Humans have wiped out the species. 2. Humans have wiped out hundreds of species of animals which once lived on our ear