I'm not sure of places in the city, but I really like De Mole in Astoria and Sunnyside. I bet they could make vegan nachos even though it's not on their normal menu. It's not a huge vegan menu, but they know what's vegan.
I go there once a week after rock climbing (Sunnyside) and they make vegan nachos for us all the time. Though their nachos are a bit different than a lot of places and a lot different than Papacitos were, they are really good in their own way.