One is a transistor, the other is a diode.
A photodiode can be operated in a number of modes, but essentially photons striking the junction allow a single electron to move across the junction.
photons striking the base junction of a phototransistor are amplified by the transistor action allowing a much higher number of electrons to travel between collector and emitter.
So you will see greater absolute changes in current if you use a phototransistor.
A photodiode may have a much faster response though (important if you need nanosecond -- or faster -- response)