I set my video mode, for standard mupen64plus, here.
/opt/retropie/configs/n64
Open mupen64plus.cfg, scroll down to ...
[Video-General]
Fullscreen = True
ScreenWidth = 320
ScreenHeight = 240
VerticalSync = False
AspectRatio = True
That is what I use for 240p on a CRT. On a LCD, change the screen size to whatever you want it to be. This works for all N64 games.