People might not like this answer, but when I was down there back in October the best nachos we had were at Margaritaville. Granted, it's not at WDW. If you're going to Universal definitely make it a point to eat there.
does chips with salsa and/or guacamole count? if yes then my vote is for la cava del tequila. we did a semi-liquid lunch...chips, salsa, guacamole, little crab tostadas and several margaritas as our lunch one day. sooooo yummy!
When we were waiting on the bridge to watch illuminations at epcot next to mexico....there was a little stand next to the mexico steps that had INCREDIBLE nachos (maybe its because i was buzzed). but they had sour cream, jalepenos, cheese, beef, tons of chips, we split it between 4 adults and a 2 year old. we loved it. it was incredible (with the frozen margaritas)
I agree with the macho nachos at the espn zone. They were excellent, real cheese not the runny stuff. I have also had the volcano nachos at margaritaville and they were good about the same as espn at the boardwalk.
Another vote for ESPN, I thought they were great although to be fair I don't think I've had them anywhere else at WDW. I like the atmosphere at ESPN too, we like to go there every trip either in the heat of the atfernoon when it is cool and fairly quiet, or for a loud fun evening
La Cantina de San Angel has an awesome guacamole, and the nacho to guacamole ratio is in favor of the guacamole, yum yum!!! I once brought that into Electric Umbrella and people keep on asking where I got it, simply because they just stopped by to eat at EU and didn't bother eating at WS ha ha ha...