A number of wave energy controllers tune the power take-off (PTO) system to the frequency of incident waves. Since real ocean waves are non-stationary by nature and not defined by a single frequency component, the PTO can be either tuned at a constant frequency characterized by the local spectrum or continuously tuned to a representative wave frequency. In either case, a time-frequency representation of the waves is expected since the wave profile changes over time. This paper discusses about the PTO tuning problem for passive and reactive controllers, in real waves, by comparing different methods for time-varying frequency estimation: the extended Kalman filter (EKF), frequency-locked loop (FLL), and Hilbert-Huang transform (HHT). The aim is to verify the impact of such methods on the absorbed and reactive powers, and the PTO rating. It is shown that the mean estimated frequency of the EKF and FLL, converges, respectively, to the mean centroid frequency and energy frequency, of the excitation force spectrum. Moreover, the HHT mean frequency has no correlation with the spectral statistical properties. A comparison of the energy absorbed shows that up to 37% more energy is obtained with the HHT over the other estimation methods. Numerical simulations are performed with sea elevation data from the Irish coast.