We present a new method for calculation of optical and magneto-optical properties of three-dimensional magnetophotonic crystal heterostructures, composed from a sequence of homogeneous plates of a magneto-optical material and photonic crystal slabs. The algorithm is based on the layer KKR technique. As examples we consider the Bi:YIG (bismuth-substituted yttrium-iron-garnet) magneto-optical plate sandwiched by photonic crystal slabs consists of (i) simple cubic/face centered cubic lattices of SiO2 spheres in the air; (ii) air spheres in silicon background (inverse opals). The enhanced Faraday rotation appears at the resonant transmission frequency in analogy with one-dimensional structures with magneto-optical microcavity. However, the calculated spectral behavior of the Faraday rotation as well as its dependence on defect thickness is quite different and unusual. For instance, the Faraday rotation angle changes its sign within the photonic band gap that is due to complicated reflection of waves from 3D photonic crystal slabs.