Agreed. I was thinking along the lines that the cities would get more votes because of population instead of the vote spread across congressional districts. Allow me to present my mea culpa.
I also agree that the threat of gerrymandering would be immense and after careful review, I would like to learn more...
Well, your original intuition was correct in that big cities tend to have more non-voters than do suburbs or rural areas, and since congressional districts are drawn based on population, not voters, cities tend to have more congressional districts than their share of the statewide vote (and thus could be said to benefit from a congressional-district presidential electoral system). However, practically speaking, even if NYC got an extra congressional district due to its non-voters, suburban and rural voters would still be better off being able to determine the winner of a reduced number of EVs than being swamped by a 90%-Democrat big city.