How to cite uproot and awkward arrays (by Jim Pivarski)? Normally a python library has a paper or user manual by the same name.
Jim Pivarski's uproot doesn't appear to, the closest thing I can find is https://arxiv.org/abs/2001.06307
Should I cite that paper or cite the github repo? (https://github.com/scikit-hep/uproot)
You can cite the paper using the arxiv number and add a link to the github repo in a footnote. As a basic example:

Methodology
In this work, we make use of the uproot package* for array
calculations [1].
* www.github.com/scikit-hep/uproot
Bibliography
[1] Pivarski et al., &quot;Awkward Arrays in Python, C++, and Numba&quot;,
arxiv: 2001.06307