In this paper we propose a saddle point approach to solve boundary control problems for the steady Navier-Stokes equations with mixed Dirichlet-Neumann boundary conditions, both in two and three dimensions. We provide a comprehensive theoretical framework to address (i) the well posedness analysis for the optimal control problem related to this system and (ii) the derivation of a system of first-order optimality conditions. We take advantage of a suitable treatment of boundary Dirichlet controls (and data) realized by means of Lagrange multipliers. In spite of the fact that this approach is rather common, a detailed analysis is still missing for mixed boundary conditions. We consider the minimization of quadratic cost (e.g., tracking-type or vorticity) functionals of the velocity. A descent method is then applied for numerical optimization, exploiting the Galerkin finite element method for the discretization of the state equations, the adjoint (Oseen) equations and the optimality equation. Numerical results are shown for simplified two-dimensional fluid flows in a tract of blood vessel where a bypass is inserted; to avoid to simulate the whole bypass configuration, we represent its action by a boundary velocity control.