How I can remove the unnecessary top padding of the Navigation view?

You can override predefined dimensions at your dimens.xml as;

<dimen name="design_navigation_padding_top_default" tools:override="true">0dp</dimen>
<dimen name="design_navigation_separator_vertical_padding" tools:override="true">0dp</dimen>
<dimen name="design_navigation_padding_bottom" tools:override="true">0dp</dimen>

Other possible values are here: https://github.com/android/platform_frameworks_support/blob/master/design/res/values/dimens.xml