Although it is generally considered accurate that 3 phase is "more efficient" than 1 phase, that is not always true. Some 1 phase motors are more efficient that some 3 phase standard motors. That said, most NEW 3 phase motors are now required to be "energy efficient" versions, and as such are almost always more efficient than 1 phase equivalents. As of yet there is no standard for an "energy efficient" 1 phase motor, so every mfr is on their own. In fact, there is a lot of disagreement as to testing methods anyway, whereas the test methods for 3 phase motor efficiency are very tight. So for all practivcal purposes one should consider 3 phase motors to be slightly more efficient that 1 phase. The transmission of electro-motive force to the load is significantly smoother as well, although that issue would be irrelevant on a pump.
All THAT said, your application presents some different issues. You said that your choices are 120V or 208V single phase, which is technically not really correct. If you have 208V, that means you have 208Y120V 3 phase service; there is no such thing as a 208/120V single phase service, only 240/120V. So if you have 208V 3 phase available, I would go with that option hands down.
First off, 1 phase motors have caps and possibly moving electrical parts that can wear out; 3 phase motors do not.
Secondly, if you were to use 208V on a 1 phase motor designed for 240V (it will NOT be designed for 208V 1 phase, no such thing), then you will be running the motor at roughly 10% undervoltage, which will put additional thermal stress on the windings, translating to lower service life.
Lastly, in using 2 poles of a 3 phase service as single phase, the phase relationship between the poles is 120 degrees. In a 1 phase service it is 180 degrees. This means if supplying a 1 phase motor with 2 phases from a 208V 3 phase system, the torque will be even more discontinuous than if supplied with a regular 240V 1 phase supply. That will also translate to thermal stress on the windings.
Bottom line, go 3 phase if you can or 120V 1 phase if you cannot.