Well to give a complete answer to this question, there are two methods: (for example we call the installed module as module1)
To remove module1 without changing package.json:
npm uninstall module1
To remove module1 with changing package.json, and removing it from the dependencies in package.json:
npm uninstall --save module1
Note: to simplify the above mentioned commands, you can use -S instead of --save , and can use remove, rm, r, un, unlink instead of uninstall