It's even worse than that.
Let's look even closer, at some of the cities, specifically New York, Los Angeles, and Chicago.
Los Angeles:
Los Angeles County
1,893,770
- 620,285
------------
1,273,485
New York
New York County
515,481
- 58,935
------------
456,546
Bronx County
318,403
- 34,424
------------
283,979
Kings County
595,086
- 133,653
------------
461,433
Queens County
473,389
- 138,550
------------
334,839
Chicago
Cook County
1,528,582
- 440,213
------------
1,088,369
Now, we add up all of those number there, and we get this:
1,273,485
456,546
283,979
461,433
334,839
+1,088,369
---------------
3,898,651
This means that from just these three cities alone, Clinton won the popular vote by about a million votes.