Make sure you're using latest NNNesterJe (v0.23), no longer updated since 2003 but still a great emulator:
http://www.emulation9.com/nnnesterj/ -> Files section -> click "english version binary etc" to download
Now start the emulator -> "Option" -> "Graphics" -> "Full Screen mode" tab:
"mode": choose your desktop res. or higher
"scaling": "Max" if want to use the whole screen area, "integer scaling if you don't.
"offscreenBuffer": "Video Memory" should make it faster
To switch between windowed and full screen modes, use [Alt]+[Enter]
Hope it helps
You can also use other emulators with nice video settings like VirtuaNes, Nestopia or FCEUltra as VampyR said