Disabling frame buffer emulation does eliminate input lag but, like you said, introduces stutter/synchronization issues and that makes the game even more irritating to play.
Another game that suffers from high input lag, Banjo-Kazooie, suffers from many graphical glitches as well, if you disable frame buffer. Oh and Banjo-Kazooie needs 7 (yes SEVEN) frames to make an action.
Even if you want to disable framebuffer, there is no such option in ParaLLel+Angrylion, this option only appears in GlideN64. And in some cases, input lag is even worse in ParaLLel. Banjo Kazooie has a staggering 8 frames of lag there. Pretty much unplayable i think.
N64 emulation suffers maybe more than any other when it comes to input lag. It’s a game by game thing though, games like Smash Bros seem to have no lag at all, regardless options.
I tried every other option available to me but the lag persists (if you use frame buffer or ParaLLel). I am convinced the issue is with the cores/emulators. Not the options. I can also feel the lag in standalone emulators. Mario 64 in particular is unplayable in PJ64 (with framebuffer ON) when playing on a LCD screen even with game mode ON (it’s hard to time the multi jumps correctly because you have to press the button before Mario lands). CRT is a bit better but still pretty bad.