Bueno, cuando voy a una heladería, normalmente la conversación va algo así:
"Buenos días! Señorita, me da un helado, por favor?"
- "Sí, claro. Con gusto. Cuál quiere?"
"Mmmm... deme una bola de helado de vainilla, por favor."
- "En un momento."
Normally, they sell them in cones, so you don't have to specify if it should come in a cup, a glass or a cone. But if you see that the store has different forms of serving scoops of ice cream, you can say:
"Deme una bola de helado de vainilla en una taza, por favor." or
"Deme una bola de helado de vainilla en un cono, por favor." or
"Deme una bola de helado en una copa (o un vaso)" (I wrote "copa", because, at least where I live, they usually call "copa" to the glass that the ice cream is served in, but if you say "vaso", they'll understand. Usually, "copa" refers to those special glasses that you drink wine or champagne in. but when it comes to ice cream, they frequently refer to the glass shaped like a cone that they use to serve ice cream as "copa")