I have a Raspberry Pi 4 running the latest version of Retropie

Which is version ... ?

[..] I deleted the Retroarch.cfg file and now NES and Snes won't allow me access in game to retroarch.

That's never a good idea, since RetroArch would then create a default configuration for the system, which trumps the RetroPie configurations and leads to all sorts of errors.

Any ideas on how to fix? Thanks in advance!

Remove the retroarch.cfg file for the NES/SNES system then immediately re-install the NES/SNES emulators so that RetroPie will add the correct RetroArch configuration - otherwise you'll get into issues again when starting from a stock RetroArch configuration.

@the496rocket please, try to fill the form in the read this first post.

There must be something wrong in your setup. RetroPie on a raspi3 with decent peripherals can run smoothly any game from the 8/16-bit era without any tweak. Just install, config input, put your ROMs and play.

[Footnote: OK, maybe 3D games, like StarFox (SNES) and Virtua Racing (Mega Drive), can stutter a bit. But the games you mentioned should work just fine.]

Both Mario Kart and Zelda run flawlessly. You may want to look into overclocking your Pi if N64 is your thing. It will smooth things out even if just a little.
Also, speaking about controllers, any dual shock or Xbox controller will do. If you don't have access to them, I'm sure you can find a second hand DS3 cheap as chips on eBay. It's a better option than a USB N64 controller, urgh... :)