Bizhawk has a port of M64+ and it seems to work well enough.

RetroArch has a port of M64+ it has support for multi-pass shaders.

There are GUIs made for it, but many are problematic and glitchy. It lacks a native GUI, and instead is ran by dragging and dropping ROMS and editing the config with notepad++.

Mupen64+ is the best overall N64 emulator, but you still need PJ64 for certain games.

Mupen64Plus is receiving far more updates, and will likely be the go-to emulator for general use in the future. Mupen64Plus improves upon Mupen64 even further, while Project64 2.1 only fixed a few things and broke others.

In terms of compatibility with the N64's game library, vanilla Mupen64 was basically always better than Project64 1.6, with 1964 basically only working well for a few different games.

Refer to this link for optimal emulator settings based on the game you want to play. Every emulator has its own unique compatibility issues, and it varies significantly even within one emulator if using different plugins. N64 emulation is a complete mess (and broken).

Best n64 emulator for pc 2020