When at open sea, one can determine the height of a wave by using various applications like a GPS system or a Swells VS system. When using the Swells VS system the height of a wave is determined by the distance between the trough and the crest indicated on the device. Check out http://www.ehow.com/facts_5745363_swell-vs_-wave-height.html for more of these details.
You could use sonar instruments to find the average depth of the ocean at that point. Then use simple trigonometry to calculate the height of the wave by knowing the angle you're looking at the wave, and the distance to the wave.
It's easy to estimate swell height from the ditch in reference to your vessel, say the bridge deck is 30ft above the waterline, if the top of the swell is higher than the bridge deck while in the ditch the swell is over 30ft tall.