I’m using the mupen64plus to play Nintendo 64. It’s running fine the game Super Mario 64, Mario Kart 64, Diddy Kong Racing and Star Fox 64. Other games is freezing and I need to reboot the Pi again. You can run N64 at full speed only Pi 2!
When You say installing Retropie, I don’t know if you download the Retropie Image File and burnt on the SD Card or installing through Raspbian. So, get the image file and the emulators and configurations were made, just need only set the file es_systems.cfg to select what emulator will use to play the systems available.
Good Luck.