Yeah Trump literally ruined Cruz's night with that response.
That's for sure. Cruz will recover from this somewhat. What hurts Cruz is that his comment was a gaffe, and one of his specific selling points was that he was not gaffe-prone. For a guy whose campaign has been extremely disciplined to date, Cruz made a remarkable error. Attacking one region of the country, even the other party's region, is never good politics; it opens you up to attacks of being a divider.
Oddly enough, if Cruz had used the phrase "Manhattan Values", he'd be receiving less flak. "New York" is both a city and a state, and this can be used against the entire GOP if he's the nominee when it comes to Congressional races and downballot races in upstate New York, and even Long Island, which lean Republican, at least.
Manhattan and small-town/rural Texas may be poles apart in outlook and values, but one of the talking points the GOP has pushed (and rightly so, IMO) is the point that the Democrats talk to Americans as members of regional, racial, ethnic, and/or special interest groups, while Republicans talk to members of regional, racial, ethnic, and special interest groups as Americans. Cruz violated this principle, and, in doing so, gave the GOP that much less credibility in that regard.