We use inelastic neutron scattering to study magnetic excitations of the FeAs-based superconductor BaFe$_{1.9}$Ni$_{0.1}$As$_2$ above and below its superconducting transition temperature $T_c=20$ K. In addition to gradually open a spin gap at the in-plane antiferromagnetic ordering wavevector $(1,0,0)$, the effect of superconductivity is to form a three dimensional resonance with clear dispersion along the c-axis direction. The intensity of the resonance develops like a superconducting order parameter, and the mode occurs at distinctively different energies at $(1,0,0)$ and $(1,0,1)$. If the resonance energy is directly associated with the superconducting gap energy $Delta$, then $Delta$ is dependent on the wavevector transfers along the c-axis. These results suggest that one must be careful in interpreting the superconducting gap energies obtained by surface sensitive probes such as scanning tunneling microscopy and angle resolved photoemission.