  Group-V materials such as niobium and tantalum have become popular choices
for extending the performance of circuit quantum electrodynamics (cQED)
platforms allowing for quantum processors and memories with reduced error rates
and more modes. The complex surface chemistry of niobium however makes
identifying the main modes of decoherence difficult at millikelvin temperatures
and single-photon powers. We use niobium coaxial quarter-wave cavities to study
the impact of etch chemistry, prolonged atmospheric exposure, and the
significance of cavity conditions prior to and during cooldown, in particular
niobium hydride evolution, on single-photon coherence. We demonstrate cavities
with quality factors of $Q_{\rm int}\gtrsim 1.4\times10^{9}$ in the
single-photon regime, a $15$ fold improvement over aluminum cavities of the
same geometry. We rigorously quantify the sensitivity of our fabrication
process to various loss mechanisms and demonstrate a $2-4\times$ reduction in
the two-level system (TLS) loss tangent and a $3-5\times$ improvement in the
residual resistivity over traditional BCP etching techniques. Finally, we
demonstrate transmon integration and coherent cavity control while maintaining
a cavity coherence of \SI{11.3}{ms}. The accessibility of our method, which can
easily be replicated in academic-lab settings, and the demonstration of its
performance mark an advancement in 3D cQED.
