The key difference is that Isochronic tones work by emitting a pulsating sound at regular intervals, whereas binaural beats use a constant sound wave format.
Because of this, many people do not like the rather intrusive and distracting sound generated by Isochronic tones, and find binaural beats more pleasurable to listen to.
However, because of this difference in delivery, Isochronic tones do not require headphones, while binaural beats do.
In terms of effectiveness. Isochronic tones are generally not as effective in the lower frequency ranges, so Binaural beats are a preferable option for Theta and Delta entrainment. There is also more scientific research to prove the efficacy of binaural beats.