We study the Stokes operator with Hodge, Navier, and Robin boundary conditions on domains \(\Omega \subseteq \mathbb {R}^d\) that are uniformly \(C^{2,1}\) . Starting with the Hodge Laplacian we etablish a bounded Hörmander functional calculus for the Stokes operator with Hodge boundary conditions. This entails a Hörmander functional calculus and boundedness of the \(H^\infty \) -calculus in spaces of soleniodal vector fields for the Stokes operator with Hodge boundary conditions. We then establish boundedness of the \(H^\infty \) -calculus for Stokes operators with Navier type conditions via Robin type perturbations of Hodge boundary conditions. This implies maximal \(L^p\) -regularity for these operators and results on fractional domain spaces. Our results cover certain non-Helmholtz domains.