Air pollution from ships has been acknowledged worldwide as a concern for several decades. Steps have been taken to reduce some of those emissions, including regulatory actions by the US EPA in the past couple of years. But emissions remain a serious problem, and new information continues to emerge.
One of the most recent findings was that tugboats have by far the highest rate of particulate emissions for the amount of fuel used, more than twice the rate of any of the other categories of ships studied by a team of NOAA and University of Colorado researchers. That's a concern both for the overall particulate emissions, and because tugboats operate near shore, increasing the pollution burden on nearby urban areas. Particulates both threaten health and contribute to climate change.
The researchers, who published their findings in the July 11, 2008, issue of the journal Geophysical Research Letters, also found that large oceangoing tankers and container ships emit particulate matter at more than twice the rate previously estimated. Other types of ships studied included ferries and large fishing boats. The study is considered the first extensive evaluation of commercial ship particulate emissions.
- NOAA press release, July 9, 2008. 
- "Light absorbing carbon emissions from commercial shipping,"  Lack et al.
For various EPA programs and regulations related to several types of emissions from vessels of many sizes, see Diesel Boats and Ships.  Some of the regulations, addressing fuels and engine emissions, are going into effect in 2007-2009.
The International Maritime Organization has been working for several years on the issue of ship emissions of many types, including particulates, nitrogen oxides, sulfur dioxide, volatile organic compounds, and greenhouse gases. For more information, see Prevention of Air Pollution from Ships. 
The US Congress recently approved legislation that moves forward US efforts to reduce ship pollution, in conjunction with international treaty requirements that soon will likely be in play (as part of the International Convention for the Prevention of Pollution from Ships, 1973, as modified by the Protocol of 1978, known as MARPOL 73/78). The President signed the legislation on July 21, 2008. For more information, search Thomas  for HR 802, the Maritime Pollution Prevention Act of 2008, or see an EPA press release of July 22, 2008. 
In harbor areas, another major pollution source is vehicles that serve ships. One starting point for covering this angle is:
For information on some of California's efforts to curb emissions in harbor areas, a starting point is:
- "California Port Fee Would Fight Pollution, Congestion,"  Los Angeles Times, July 16, 2008, by Nancy Vogel.
You can likely glean some additional starting points here.