This paper introduces the Quantum Covariance Embedding, which embeds Positive Operator-Valued Measures into a tensor product of a Reproducing Kernel Hilbert Space and the quantum state space via a tensorized Bochner integral. This construction induces the Quantum Maximum Discrepancy that metrizes the space of quantum measurements. Applying this framework to Quantum State Tomography, we reformulate density estimation as a tensorized kernel regression, enabling optimal inference without the basis-dependent sparsity constraints that restrict existing methods. We develop a unified geometric design theory for quantum Gram superoperators, establishing that Unitary Designs are strictly E-optimal experimental designs and thus statistically superior to Pauli observables. For general structure-free estimation, we derive the exact minimax lower bound and prove that our tensorized estimators achieve this optimal rate. Furthermore, we introduce the QUAntum Regression with Kernels (QUARK) estimator to accommodate the spectral geometry of physical implementations, deriving central limit theorem and concentration inequalities. To facilitate practical estimation, we establish the exactness of trace-preserving projections and demonstrate efficient estimation under mutually unbiased bases via the fast Walsh-Hadamard transform.