The dissociation of quarkonia in the medium created in heavy ion collisions is still one of the most debated topics in the heavy ion community. Progress in understanding the effect relies on a broad range of measurements in collisions with different nuclear sizes, covering a broad rapidity range. This presentation will report the $J/\psi$ measurements performed by the PHENIX collaboration at forward and backward rapidities of 1.2 $< |y| <$ 2.2 in $p$+Al, $p$+Au, and $^3$He+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV, and the corresponding nuclear modification factors.