We consider superintegrability in classical mechanics in the presence of magnetic fields. We focus on three-dimensional systems which are separable in Cartesian coordinates. We construct all possible minimally and maximally superintegrable systems in this class with additional integrals quadratic in the momenta. Together with the results of our previous paper [J. Phys. A: Math. Theor. 50 (2017), 245202, 24 pages], where one of the additional integrals was by assumption linear, we conclude the classification of three-dimensional quadratically minimally and maximally superintegrable systems separable in Cartesian coordinates. We also describe two particular methods for constructing superintegrable systems with higher-order integrals.