<p>Electron-phonon coupling is a key interaction that governs diverse physical processes such as carrier transport, superconductivity, and optical absorption. Calculating such interactions from first-principles with methods beyond density-functional theory  remains a challenge. We introduce here a finite-difference framework for computing electron-phonon couplings for any electronic structure method that provides eigenvalues and eigenvectors, and showcase applications for hybrid and Koopmans functionals, and $GW$ many-body perturbation theory. Our approach introduces a novel projectability scheme based on eigenvalue differences and bypasses many of the limitations of the direct finite difference methods. It also leverages symmetries to reduce the number of independent atomic displacements, thereby keeping computational costs manageable. This approach enables seamless integration with established first-principles codes for generating displaced supercells, performing Wannier interpolations, and evaluating transport properties. Applications to silicon and gallium arsenide show that advanced electronic-structure functionals predict different electron-phonon couplings and modify band curvatures, resulting in much more accurate estimates of intrinsic carrier drift mobilities and effective masses. In general, our method provides a robust and accessible framework for exploring electron-phonon interactions in complex materials with state-of-the-art electronic structure methods.</p>