You mean the auxiliary 'do'?
Do is used to from questions, for negation or for emphasis.

Even though this is a question, do isn't needed because which makes it a question. Without the which, if you were asking about a particular bus, "Does this bus go to New York?"

In your sentence, it could be changed to "Which bus does go to New York?" This would add emphasis, in other words it's like saying, "Okay, this bus doesn't go to New York and neither does that one, which one *does* go to New York.?"

And for negation, "Which bus does not go to New York?"

There is a subject, object and verb. You are good to go.