Across the nation, Trump won over 2600 counties and Hillary won less than 500.
If you subtract out just 6 counties, Trump wins the popular vote by almost 70,000 votes.
-------------------------------------------- Clinton ---------- Trump
LA county-----------------------------1,893,770 ------- 620,285
Manhattan-------------------------------515,481 --------- 58,935
Queens---------------------------------- 473,389 --------138,550
Westchester -------------------------- 245,670 --------121,643
Bronx ------------------------------------ 318,403 --------- 34,424
Brooklyn -------------------------------- 595,086 ------- 133,653
Total ----------------------------------- 4,041,799 ----- 1,107,490
Nationwide ------------------------ 65,844,610 — 62,979,636
Nationwide w/o 6 counties — 61,802,811 — 61,872,146
So if you want NY city and LA controlling who is is president, then change to a popular vote system. The electoral college was set up in the constitution so that states with small populations would have at least some say in the presidential election.
Source: NY Times data by county
nytimes.com/elections/results/president