The instantaneous frequency (IF) of a non-stationary signal is usually estimated from a time-frequency distribution (TFD). The IF of heart rate variability (HRV) is an important parameter because the power in a frequency band around the IF can be used for the interpretation and analysis of the respiratory rate but also for a more accurate analysis of heart rate (HR) signals. In this study, we compare the performance of five states of the art kernel-based time-frequency distributions (TFDs) in terms of their ability to accurately estimate the IF of HR signals. The selected TFDs include three widely used fixed kernel methods: the modified B distribution, the S-method and the spectrogram; and two adaptive kernel methods: the adaptive optimal kernel TFD and the recently developed adaptive directional TFD. The IF of the respiratory signal, which is usually easier to estimate as the respiratory signal is a mono-component with small amplitude variations with time, is used as a reference to examine the accuracy of the HRV IF estimates. Experimental results indicate that the most reliable estimates are obtained using the adaptive directional TFD in comparison to other commonly used methods such as the adaptive optimal kernel TFD and the modified B distribution.