Due to the lack of free neutron targets, studies of the structure of the neutron are typically made by scattering electrons from either $^2$H or $^3$He targets. In order to extract useful neutron information from a $^3$He target, one must understand how the neutron in a $^3$He system differs from a free neutron by taking into account nuclear effects such as final state interactions and meson exchange currents. The target single spin asymmetry $A_y^0$ is an ideal probe of such effects, as any deviation from zero indicates effects beyond plane wave impulse approximation. New measurements of the target single spin asymmetry $A_y^0$ at $Q^2$ of 0.46 and 0.96 (GeV/$c)^2$ were made at Jefferson Lab using the quasi-elastic $^3mathrm{He}^{uparrow}(e,en)$ reaction. Our measured asymmetry decreases rapidly, from $>20%$ at $Q^2=0.46$ (GeV/$c)^2$ to nearly zero at $Q^2=0.96$ (GeV$/c)^2$, demonstrating the fall-off of the reaction mechanism effects as $Q^2$ increases. We also observed a small $epsilon$-dependent increase in $A_y^0$ compared to previous measurements, particularly at moderate $Q^2$. This indicates that upcoming high $Q^2$ measurements from the Jefferson Lab 12 GeV program can cleanly probe neutron structure from polarized $^3$He using plane wave impulse approximation.