Autonomous underwater vehicles operating near the sea surface are subject to wave disturbances in their motion, which can affect severely the data acquisition during the vehicle motion. Bathymetric maps, for example, may suffer a big loss in quality due to such kind of disturbances that can impose oscillations in the vehicle depth and attitude. This article describes a controller structure for compensating the wave disturbances in the vertical plane for a torpedo-like autonomous underwater vehicle, based on a modified version of the linear quadratic Gaussian with loop transfer recovery control combined with a wave filter. The proposed methodology uses additional to the classic linear quadratic Gaussian with loop transfer recovery design the measurement of non-controlled states, such as the pitch rate and heave velocity, in the control action. The wave disturbances were filtered away by a shaping filter fitted to the sea spectrum, and the sensor signals were integrated by an extended Kalman filter. The proposed control methodology was tested against the classical linear quadratic Gaussian with loop transfer recovery controller in a 6-degree-of-freedom non-linear autonomous underwater vehicle simulator, producing a better performance in most demanding conditions such high wave crests. The tests also revealed the impact of the hydroplane geometry on the controller performance, which should not be underestimated by the autopilot designer.