We develop a Discrete Duality Finite Volume (\DDFV{}) method for the three-dimensional steady Stokes problem with a variable viscosity coefficient on polyhedral meshes. Under very general assumptions on the mesh, which may admit non-convex and non-conforming polyhedrons, we prove the stability and well-posedness of the scheme. We also prove the convergence of the numerical approximation to the velocity, velocity gradient and pressure, and derive a priori estimates for the corresponding approximation error. Final numerical experiments confirm the theoretical predictions.