You could try it with another TV (e.g. Sony KDL-40W4000 which has a really low input lag, but it is a very old model. Newer models like for example KDL-50W800B also have a low input lag on game mode), or you could test a bluetooth dongle (to test, if the input lag is caused by the internal bluetooth of the Pi3), or you could test with another controller (PS3 controller for example), to test, if the input lag is caused by the NES30 Pro.
But compared to a real console, emulation always produce a bit of input lag.
