There could be an extra Tab "Whitespace" in Tools->Options->Fonts&Colors with a listbox on the left with three items:
On the right there would be a checkbox whether particular highlight is applied or not and a highlight configuration like under "Syntax" tab.
However I somewhat resist to put this under Syntax tab since it's not related to syntax of the language and it would not be turnable on/off. Highlighting tab does not offer font (or effects) change which could be beneficial here since it would be applied to the font of non-visible chars display.
Current solution are items in Tools->Options->Fonts&Colors->Highlighting tab:
When assigning background colors to them the indentation/trailing whitespace will start to be shown.
Integrated into 'main-golden', will be available in build *201305172300* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
User: Miloslav Metelka <email@example.com>
Log: #225747 - Allow more detailed control of whitespace and newline highlighting.
*** Bug 205854 has been marked as a duplicate of this bug. ***
*** Bug 205247 has been marked as a duplicate of this bug. ***