This paper is concerned with numerical methods for the Navier-Stokes-Nernst-Planck-Poisson equation system. The main goal is to construct and analyze some stable time stepping schemes for the time discretization and use a spectral method for the spatial discretization. The main contribution of the paper includes: 1) an useful stability inequality for the weak solution is derived; 2) a first order time stepping scheme is constructed, and the non-negativity of the concentration components of the discrete solution is proved. This is an important property since the exact solution shares the same property. Moreover, the stability of the scheme is established, together with a stability condition on the time step size; 3) a modified first order scheme is proposed in order to decouple the calculation of the velocity and pressure in the fluid field. This new scheme equally preserves the non-negativity of the discrete concentration solution, and is stable under a similar stability condition; 4) a stabilization technique is introduced to make the above mentioned schemes stable without restriction condition on the time step size; 5) finally, we construct a second order finite difference scheme in time and spectral discretization in space. The numerical tests carried out in the paper show that all the proposed schemes possess some desirable properties, such as conditionally/unconditionally stability, first/second order convergence, non-negativity of the discrete concentrations, and so on.