"there is nothing in the PyPI package description that actually indicates what version of Python is being targeted"
is incorrect. There are Trove classifiers[1] for both versions, and indeed for every minor version number of both versions. There are even Python 2 and 3 classifiers that end in "Only", which look like they would exactly fit the author's use case.
However, since pip 9.0.0, it will respect the Requires-Python[0] metadata, which can be specified via your setup.py file.
Since PyPI allows only a single source distribution per release, though, this will still not get you separate modules for separate codebases as it seems you originally desired. As mentioned in a previous comment, it's generally preferred to support multiple versions in a single codebase via six.
[0]: https://www.python.org/dev/peps/pep-0345/#requires-python