A three-dimensional frequency-domain numerical wave tank (FR-NWT) based on the Rankine panel method was developed. An optimal artificial damping zone (ADZ) scheme was first applied to the FR-NWT to prevent reflection waves from the end walls. Parametric studies of ramp function shape with artificial damping coefficients and damping zone length were conducted to find a proper damping scheme for the frequency domain program. Applying both the Sommerfeld radiation condition and the ADZ scheme to the frequency domain program can reduce the length of the ADZ to less than one wavelength. The FR-NWT developed by the authors was used to calculate the hydrodynamic response of a hemispherical-heaving buoy wave energy converter (WEC) integrated with a seawall-type breakwater of infinite length. A linear power take-off system was used to calculate power generation of the WEC. The global motion of the WEC combined with the breakwater was up to 1.85 times greater than that of the WEC without the breakwater. Moreover, the capture width ratio of the WEC increased approximately 3.67 times more than that of the WEC without the breakwater.