There are a variety of pitch detection methods ranging in sophistication from counting zero-crossing (which obviously won't work in your case) to extremely complex algorithms.
While the frequency domain methods seems most appropriate, it's not as simple as "taking the FFT". If your data is very noisy, you may have spurious peaks that are higher than what you would consider to be the dominant frequency. One solution is use window overlapping segments of your signal, and do STFTs, and average the results. But this raises more questions: how big should the windows be? In this case, it depends on how far apart you expect those dominant peaks to be, how long your recordings are, etc. (Note: FFT methods can resolve to better than one-bin size by taking into account phase information. In this case, you would have to do something more complex than averaging all your FFT windows together).
Another approach would be a time-domain method, such as YIN:
http://recherche.ircam.fr/equipes/pcm/cheveign/pss/2002_JASA_YIN.pdf
Wikipedia discusses some more methods:
http://en.wikipedia.org/wiki/Pitch_detection_algorithm
You can also explore some more methods in chapter 9 of this book:
http://www.amazon.com/DAFX-Digital-Udo-ouml-lzer/dp/0471490784
You can get matlab sourcecode for yin from chapter 9 of that book here:
http://www2.hsu-hh.de/ant/dafx2002/DAFX_Book_Page_2nd_edition/matlab.html