The Goertzel algorithm http://www.embedded.com/design/configurable-systems/4024443/The-Goertzel-Algorithm is a fairly efficient tone detection method that resolves the signal into real and imaginary components. I'll assume you can do the numeric to get the phase difference or just polarity, as you require.
Resolution versus time constant is a design tradeoff which this article highlights issues. http://www.mstarlabs.com/dsp/goertzel/goertzel.html
Additional
"What accuracy can be obtained?"
It depends...upon what you are faced with (i.e., signal levels, external noise, etc.), what hardware you have (i.e., adc, processor, etc.), and how you implement your solution (sample rate, numerical precision, etc.). Without the complete picture, I'll be guessing what you could achieve as the Goertzel approach is far from easy.
But I imagine for a high school project with good signal levels and low noise, an easier method of using the phase comparator (2 as it locks at zero degrees) of a 4046 PLL www.nxp.com/documents/data_sheet/HEF4046B.pdf will likely get you down to a few degrees.
One other issue if you have a high Q transducer is generating a high-resolution frequency. There is a method but that's another avenue.
Yet more
"Harmonics of Fundamental (Which might be significant)"... hmm hence the digital filtering; but if the sampling rate is too low then there might be a problem with aliasing. Also, mismatched anti-aliasing filters are likely to take your whole error budget. A rule of thumb of ten times sampling frequency seems a bit low, and it being higher it will make the filter design easier.
Spatial windowing addresses off-frequency issues along with higher roll-off and attenuation and is described in this article. Sliding Spectrum Analysis by Eric Jacobsen and Richard Lyons in Streamlining Digital Signal Processing http://www.amazon.com/Streamlining-Digital-Signal-Processing-Guidebook/dp/1118278380
In my previous project after detecting either carrier, I then was interested in the timing of the frequency changes in immense noise. With carrier phase generation inconstancies, the phase error was never quiescent to be quantified, so I can't guess better than you what you might get with your project conditions.