Numerical solution strategies for the Stokes eigenvalue problem based on the use of penalty formulations are investigated in this study. It is shown that the penalty method approach can successfully be adapted for the eigenproblem to rectify the associated problems such as the existence of zero diagonal entries in the resulting algebraic system. Two different schemes, namely, the standard penalisation with a small penalty parameter, and the iterative penalisation that enables relatively large parameters, are implemented. The employment of the latter leads to a so-called inhomogeneous generalised eigenvalue problem which requires a special attention. A feasible solution strategy is presented which is adapted from a procedure based on Newton's method proposed for the corresponding standard (inhomogeneous) eigenvalue problems. Concerning the spatial discretisation, among other possible options, the Chebyshev spectral collocation method based on expanding the unknown fields in tensor product of Chebyshev polynomials is employed. It is shown that the method constitutes a novel way of efficiently examining the approximate eigensolutions of the Stokes operator with the use of Chebyshev spectral collocation method directly, without a decoupling of velocity and pressure.