In a previous study, three-dimensional (3D) linear and simplified nonlinear finite-element soil response methods based on a horizontal-component input seismic wave field were proposed. A seismic wave field means seismic waves propagating in a 3D medium. The method had been developed with the goal of adequately treating short-period (less than a few seconds) seismic surface waves trapped by a deep (several km) underground structure in a shallow soil model. In the present study, along with improvements of the methods, 3D linear and simplified nonlinear soil response methods based on a three-component input seismic wave field are developed, and are applied to estimate seismic soil responses in the three geotechnical zones (the reclaimed, alluvial, and hill zones) of Tokyo during two large earthquakes. The more reasonable soil responses revealed that, in a practical sense, vertical ground motions affected soil responses very little. They also clarified large effects of liquefaction in the reclaimed zone and inferred no large ground failure in the alluvial and hill zones.