'Margherita' is a somewhat confusing term that has multiple meanings. It can be the traditional Neapolitan pizza with only tomatoes, cheese and basil, or it can be used in New York/Quasi New York establishments to usually signify a plan pie with basil, but the definition is a bit looser. For NY places, it's more of a marketing term, and, imo, a poor marketing term at that. Misguided owners try to class up the place while losing sight of the humble yet glorious potential of a plain slice. I don't automatically walk out when I see it on the menu, but it's a pretty huge black mark.
It's a Neapolitan term, through and through, and should only be utilized in the Neapolitan style arena. It has no place in non coal NY style pizzerias (coal get's a little more leeway because of it's history/ties to Neapolitan pizza).