[link|http://www.census.gov/population/documentation/twps0027/tab22.txt|Population of the 100 Largest Urban Places: 1990]: New York City, Los Angeles, Chicago (via GL/SLS), Houston, Philadelphia, San Diego, Detroit.
The first non-port is Dallas, it's followed by Phoenix and San Antonio. San Jose, part of the San Francisco - Oakland - San Jose conurbanation, hosting three major and several minor ports. The list continues to list Baltimore, San Francisco, Jacksonville, Memphis, Washington DC, Boston, and Seattle, in the 21 largest cities, all with ports or deep water sea access (including river access in some cases).
As much as we think of this as a modern age, the traditional mode of lugging things around by floating them over water is still a tremendously effective transportation mode. Too, marine climates are often more hospitable than inland ones.
There's also the mitigating fact that some urban areas are actually significantly inland. The Port of Los Angeles is connected to the city via a long thread of land. The city of San Diego now sprawls considerably inland, though downtown does lie proximate to the harbor. Seattle, OTOH, is completely surrounded by water, as is the SF Bay Area.