Could some one please help with differences between those two screen readers? As I was faced with one issue while testing the accessibility using them. Of course, I fixed the issue with screen reader only (Bootstrap's class to span element to read the sort order).
There are a lot of ways to answer this question. It partly depends on version and with which web browser the screen reader is paired. In short, that matrix can make it pretty complex to identify all the differences.
For example, CSS is handled differently by different screen readers: http://webaim.org/blog/screen-readers-and-css/
Or take a look at the HTML / ARIA / WCAG tracking PowerMapper does: https://www.powermapper.com/tests/screen-readers/
Perhaps most relevant to most users is that NVDA is free and JAWS is not.
If there is a specific issue you are trying to address, then you should just ask that question instead.