This paper deals with the numerical optimization of the first three eigenvalues of the Laplace-Beltrami operator of domain in the Euclidean sphere in $\mathbb{R}^3$ with Neumann boundary conditions. We address two approaches : the first one is a generalization of the initial problem leading to a density method and the other one is a shape optimization procedure via the level-set method. The original goal of those method was to investigate the conjecture according to which the geodesic ball were optimal for the first non-trivial eigenvalue under certain conditions. These computations give some strong insight on the optimal shapes of those eigenvalue problems and show a rich variety of shapes regarding the proportion of the surface area of the sphere occupied by the domain. In a last part, the same algorithms are used to carry the same survey on a torus.