We have used polarized Raman scattering to probe lattice vibrations and charge ordering in 12 nm thick, epitaxially strained PrNiO$_3$ films, and in superlattices of PrNiO$_3$ with the band-insulator PrAlO$_3$. A carefully adjusted confocal geometry was used to eliminate the substrate contribution to the Raman spectra. In films and superlattices under tensile strain, which undergo a metal-insulator transition upon cooling, the Raman spectra reveal phonon modes characteristic of charge ordering. These anomalous phonons do not appear in compressively strained films, which remain metallic at all temperatures. For superlattices under compressive strain, the Raman spectra show no evidence of anomalous phonons indicative of charge ordering, while complementary resonant x-ray scattering experiments reveal antiferromagnetic order associated with a modest increase in resistivity upon cooling. This confirms theoretical predictions of a spin density wave phase driven by spatial confinement of the conduction electrons.