The number of deaths fell to 55,391 in 2006 from 57,068 a year earlier, according to the city's Health Department of Health and Mental Hygiene. The only leading killer that increased significantly was substance use, up 8 percent.
Heart disease and cancer remained the most deadly, claiming 21,844 and 13,116 lives, respectively.
Between 2005 and 2006, death from HIV fell almost 15 percent, from 1,419 to 1,209, reflecting the lowest numbers since 1984 when 952 deaths from AIDS were recorded citywide.
Researchers attributed the decline to lower infection rates because of syringe exchange programs, expanded HIV testing, and slower disease progression.
HIV mortality remains concentrated among the city's minority populations, with roughly 34 percent of deaths among black men; 21 percent among black women; 11 percent among white men; and 3 percent among white women.
New HIV diagnoses have recently increased among young men who have sex with men, but the trend has yet to affect mortality rates.
All smoking-related deaths dropped 11.2 percent between 2002 and 2006, from 8,722 to 7,744. The figures do not include deaths from exposure to second-hand smoke.
The report also showed that life expectancy for women between 2004 and 2005 rose by 2.5 months to 81.3 years, while male life expectancy remained unchanged at 75.7 years. Overall life expectancy rose to 78.7 years from 78.6 years.