In this paper, we propose a unified non-conforming least-squares spectral element ap- proach for solving Stokes equations with various non-standard boundary conditions. Ex- isting least-squares formulations mostly deal with Dirichlet boundary conditions and are formulated using ADN theory based regularity estimates. However, changing boundary conditions lead to a search for parameters satisfying supplementing and complimenting con- ditions [4] which is not easy always. Here we have avoided ADN theory based regularity estimates and proposed a unified approach for dealing with various boundary conditions. Stability estimates and error estimates have been discussed. Numerical results displaying exponential accuracy have been presented for both two and three dimensional cases with various boundary conditions.