I heard that a lot of people use Nestopia, because it has minimal input lag. I want to run SMB1 on Nestopia too, but sometimes it makes small lag spikes. It's not that bad, but in some places it can be hard to do frame perfect inputs with this. Furthermore, most people don't have that issue. Can somebody tell me what can be wrong?

I don't really know, other than your computer being slow? Nestopia seems to be the one that runs BEST for most people. BizHawk and FCEUX gave me really weird lag spikes.

I'm currently using BizHawk, and it doesn't make any lag spikes, even while recording in 60 FPS.