ES6 modules export JavaScript elements per file. This is a low level module concept on basis of the programming language without any semantic meaning.
Angular modules define modules in the semantics of Angular as a framework for building single page web/mobile apps. An Angular module defines which Angular specific elements
- belong together,
- are exported and
- are imported.
Some may think that the above comparsion is superfluous because the difference is quite clear, but I found some so called 'professional' articles that lack clear statements, like the following I found describing Angular modules in short:
"Modules are blocks of code that do a certain type of task. A module exports some value in the main code, such as class. The first and the most common module that you will study is the one that exports Component Class."
This explains ES6 modules that are part of the language but not the Angular module concept in any way.
Update, 03/01/2017:
Here are some sources about the topics:
Javascript and Modules
Angular Modules