The huge ships that travel in and out of US ports, and the cargo handling equipment and trucks that operate there, are a significant source of air pollution. The Apr. 15, 2009, TipSheet  reported an EPA move to force all ships docking at US ports to conform to US air quality standards. But many more efforts by coastal state governments, local governments, and local air quality agencies are pushing ahead with their own regulations and mitigation efforts.
On June 30, 2009, a federal court judge rejected a Pacific Merchant Shipping Association request for a summary judgment that would have blocked California Air Resources Board regulations requiring ships to use low-sulfur fuel within 24 nautical miles of the coast (Courthouse News Service story ). The CARB regulation went into effect July 1, 2009. 
The Cunningham Report noted a potential safety issue  related to the switch to maritime low-sulfur fuels. Some pilots are reporting that the fuel causes sputtering and stalling, which can make it more difficult or dangerous to navigate through crowded ports. If you live near a port, check with your local merchant marine association for pilots' opinions on whether low-sulfur fuel presents special mechanical or navigational challenges.
Also in California, Assembly member Jerry Hill (D-San Mateo) has introduced bill 1431 (currently before the Assembly Transportation Committee) that would harmonize emission reduction strategies for the Port of Oakland with those of ports in Los Angeles and Long Beach. It would also require the Bay Area Air Quality Management District, CA Air Resources Board, and the SouthCoast Air Quality Management District to cooperate to impose a "state mandated local program."
Puget Sound Clean Air Agency has a variety of initiatives aimed at reducing shipping-related emissions  for the ports of Seattle, Tacoma, and Everett. Grants from EPA and the ports  are helping to fund these measures.
There are also new efforts on the federal level to clean up the air around ports: EPA's new proposed rules for oceangoing vessels  would require that new ships are equipped with engine technologies that reduce nitrogen oxide emissions beginning in 2011. More stringent nitrogen oxide standards would go into effect in 2016.
The EPA rules would also prohibit marine fuel oil containing over 1,000 parts per million (ppm) of sulfur from being produced or sold for use in the 230-mile long U.S. Emission Control Area (ECA) which would extend 200 nautical miles inland from U.S. and Canadian coastlines. The ECA would apply to all ships entering the area. If approved, the ECA could go into effect as early as 2012.
The International Maritime Organization is currently holding its environment meeting in London,  where these and other issues are being considered; email.  At the meeting, the IMO adopted voluntary standards for reducing greenhouse gas emissions from ships. 
A 2009 report from Energy Futures, "US Container Ports and Air Pollution, A Perfect Storm,"  provides context on air pollution around the 10 largest US ports. Author: James S. Cannon,  303-541-0185.