If he has the same powers and power levels as Superman, where was he when... take your pick and insert any major Doctor Who or real-world event of the last few years or indeed to come.
Where were UNIT or Torchwood during the incidents from The Sarah Jane Adventures or Class? This is the kind of question that comes up in any such shared universe, and usually you just have to shrug it off and assume the other guys were busy elsewhere. In this case, the fact that the Ghost operates in New York may explain it, because the Doctor's Earth-based adventures are usually in the UK, and he hasn't been able to get to New York for a while now.
Then again, maybe it's a timeline change. Modern Doctor Who seems to assume that history is constantly changing due to the interventions of time travelers, that only certain "fixed points" remain constant. The Twelfth Doctor created a new path for history by giving Grant that crystal, so the Ghost wouldn't have existed in any of the Doctor's prior adventures.