We propose an unsupervised regularized inversion method for reconstruction of the 3D refractive index map of a sample in tomographic diffractive microscopy. It is based on the minimization of the generalized Stein's unbiased risk estimator (GSURE) to automatically estimate optimal values for the hyperparameters of one or several regularization terms (sparsity, edge-preserving smoothness, total variation). We evaluate the performance of our approach on simulated and experimental limited-view data. Our results show that GSURE is an efficient criterion to find suitable regularization weights, which is a critical task, particularly in the context of reducing the amount of required data to allow faster yet efficient acquisitions and reconstructions.