Cross-correlation methods were applied for the estimation of the power spectral density and modulation spectrum of underwater noise generated by moving vessels. The cross-correlation of the signal from two hydrophones allows the separation of vessel acoustic signatures in a busy estuary. Experimental data recorded in the Hudson River are used for demonstration that cross-correlation method measured the same ship noise and ship noise modulation spectra as conventional methods. The cross-correlation method was then applied for the separation of the acoustic signatures of two ships present simultaneously. Presented methods can be useful for ship traffic monitoring and small ship classification, even in noisy harbor environments.