The easiest way to get wave parameters from the accelerometer will be to transform the accelerations to Fourier space using the FFT, then integrate simply by multiplying by the frequencies (twice). This will give the power spectral density (PSD) of the waves. Now, discard the low frequency part of the signal (periods longer than 15 s, say) and integrate under the remaining spectrum to get the spectral moments:
M0 = integral (PSD * df)
M1 = integral (PSD *f *df)
M2 = integral (PSD *f^2 * df)
etc
Whence the wave parameters:
Hs = 4sqrt(M0) significant wave height
TM1= M0/M1 mean period
SW = 1 - M2^2/(M0M4) spectral width
etc
The elegant thing about this method is that we never have to process the time series.