So this is odd: According to a new study by the U.S. Census Bureau, the four densest "urbanized areas" of the country are now all in California, and Los Angeles and the Bay Area at the top of the list. San Jose comes in third, but the fourth-place winner, which is technically more dense by this measure than New York City, is Delano, California a backwater down on Highway 99 near Bakersfield with two prisons, a tiny airport, and a population of 54,372.
But see, here's the thing with this measure of density and this definition of "urbanized area": it takes the whole area as defined by its "integrated job market," and looks at cities and towns with populations over 50,000. So New York City and Newark, NJ (which are grouped together for these purposes) comprise multiple cities and towns across a 3,450-square-mile area, including some rural parts of Connecticut and almost all of Long Island. Thus, the New York-Newark area comes in fifth, behind Delano, which is small but which has the most people living within its boundaries of any city of its size (maybe because of those prisons!?!).
As architecture critic John King explains in the Chronicle, while Manhattan may be loads denser than any part of the Bay Area, our planning codes over the years have kept our density hemmed in to strictly defined areas, with rural area and park land distinctly excluded, so therefore when you look at average density we have 6,266 people per square mile, compared to New York-Newark's 5,319.
See the full roster here, and you'll see that 7 of the 10 densest urban areas are all in CA now.