"not chocolate" ;-)
I guess you could try saying that you'd like a "plain" milkshake, and you'd probably end up with vanilla.
Well, you have two options:
1) Point at the menu. (I do this!)
2) Learn the V and L sounds in English. I realise that it's difficult because some English sounds don't exist in Japanese (such as V!), but ask a friend to show you, then practise. That's really the best and easiest way. :)