The NES soundfonts aren't very good, mainly for the fact that the samples aren't really simple waveforms, some of the samples even have attacks on them, and that is just no no no. The quality of the waveforms is bad, not as clear as if you use better samples or a VSTi that actually generates the sound itself.
Also yeah, there's different types of square waves you can use, with different types of width to them to sound a bit different.
I should probably tell you right now that I'm pretty anal about this sort of thing - I'm kind of a chiptune "purist" so if someone calls their song a NES chiptune that they made in FL Studio, I get into RAGE mode and remind them what NES is supposed to sound like. Most people won't respond that way though, as long as the song is good, or fun, or whatever