Both types have a lot in common, as they share decision making functions, but that's a topic for another thread. This is my understanding of the differences between the two:
ESTJs are practical, highly competent and the ideal employee for the majority of companies. When they're being brutally honest and bossy and hurting people's feelings, they may well notice thanks to their strong sensing side, and back off. Their Te-Si makes them extremely talented at creating highly efficient and highly practical systems based on their experience, and their Ne causes them to frequently break from the norm to attempt new ideas. Their main weakness is a lack of timing and foresight and frequently jumping into things without considering the long term consequences. Bright ESTJs make exceptional accountants, and they're often in all levels of management.
ENTJs are innovative, strategic and forceful. They have great foresight, and generally know when they do not need to act. An ENTJ is likely to get carried away in a forceful show of Se, and to hurt people through it without being fully aware of the damage they're doing. However, thanks to Ni, they'll often reflect on this later and look at it from different perspectives, inevitably realising their fault and learning from it. ENTJs are also great at evaluating the strengths and weaknesses of others, making them great at people management. Ni makes an ENTJ quite laid back, but Se drives them to be forceful, making them quite capable of a sudden complete personality turnaround.