Hot film aneomemeter will work, if you can traverse it under way. However they foul easily and have a potential for flow pertubration. A better way mightbe laser doppler velocimeter.. but it would be a $ 50-200K instrument depending upon how many components of velocity you would want to measure. I built them commercially for 15 years, including 3 component ones used in tow tanks for sub development and always wanted to apply it a race boat. However both Hot film and LDV are single point measurements, so unless you want to measure velocity (and determine turbulence over a period of time) you need to move the measurement point. . IAnother option might be Particle Image Velocimetry, with can do a 2D plane, but it is not cheap either and would be pretty tricky to setup on a mving boat.
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