When looking for health statistics, it may be useful to keep in mind a few rules of thumb:

It takes time to compile information.  Sometimes  the most recent statistical data will be 3 or more years old. Check the sources of statistics that you find.  If you need more detail, you may be able to contact the agency, organization, or company that prepared the data. Sometimes you may not be able to locate figures at a municipal or even a county level.  If you absolutely need more local data, you may have to contact the local health department directly to find out if the information is available. It is usually easier to find data on "reportable" diseases.  Health care providers are required to provide statistics on them.

New Jersey State Sources

Communicable Diseases Service Statistics (NJ Department of Health and Senior Services)

New Jersey Center for Health Statistics
The New Jersey Center for Health Statistics is your source for state and local (primarily by county) statistics.

New Jersey Health Statistics from 1877 to 2000: An Historical Electronic Compendium of Published Reports
This compendium is an enormous archive of official annual reports on the health of New Jersey, including extensive compilations of population-based health statistics, which covers over 45,000 pages of original content in the 141 separate documents that it incorporates. Spanning three centuries and the entire series of printed documents from 1877 to 2000, all of the original reports had been initially prepared as government publications.

Births by Municipality (NJ Center for Health Statistics)
Covers 1989-1997.  Check New Jersey Health Statistics for 1998 and onward.

Behavioral Risk Factor Surveillance System (BRFSS) (NJ Center for Health Statistics) 
Figures for New Jersey adults on a number of health issues appear here.

Cancer Among Hispanics In New Jersey, 1990-1996 (NJ Office of Cancer Epidemiology)
Statistics by race/ethnicity (Hispanics, Non-Hispanic Whites, and Blacks), gender, and age. 

County Health Status Profiles (NJ Center for Health Statistics)
Population by age, natality, mortality, and morbidity.  Covers 1996, 1998, and 2000.

Drug and Alcohol Use Among New Jersey High School Students (NJ Department of Law & Public Safety, Division of Criminal Justice)
Covers 1980-1998.

Health Insurance Coverage in New Jersey (NJ Center for Health Statistics)
Figures by age, race, income, employment, education, and sex.  Covers 1995-2004.

New Jersey Health Statistics (NJ Center for Health Statistics) 
Population, marriage & divorce, natality (births), morbidity (diseases), and mortality (deaths).  Covers 1993-2003.

New Jersey Vaccine Preventable Childhood Diseases Preliminary 2000 Morbidity By County - Data on Pertussis, Measles, Mumps, Rubella, Tetanus, Diphtheria, Polio, and Hib. Also available for 1999 (Preliminary), 1998, 1997, 1996.

Healthy New Jersey 2010 State Health Issues Opinion Survey (NJ Department of Health and Senior Services)
Results of a public opinion poll of views on health issues. Conducted by the Eagleton Institute.

New Jersey State Cancer Registry (NJ Department of Health and Senior Services)
Data covers 1979-1998, depending on the table.

Then and Now in New Jersey: Health Profiles for 1900 and 2000 - (NJ Center for Health Statistics) Interesting statistics about the life, illnesses and deaths of persons living in New Jersey contrasted with those living in the state in 2000.

Traumatic Brain Injury in New Jersey (NJ Center for Health Statistics)
Covers 1994.

Update Healthy New Jersey 2000 - Second Update and Review (NJ Department of Health and Senior Services)
Information on preventive and primary care (1985-97); infant, child, and maternal health (1985-98); adolescent health (1980-96); cancer (1985-97); cardiovascular and other vascular diseases (1985-97); AIDS (1988-97); sexually transmitted diseases (1985-97); infectious diseases (1985-97); injuries (1985-97); occupational & environmental hazards (1983-97); addiction (1980-97); and causes of death by age group (1996).  Note that dates of coverage vary by table.

CAMConnect - CAMConnect: Linking Communities with Information is devoted to creating a learning partnership in Camden, New Jersey, with the belief that sharing and using data will lead to informed decisions and better policy making to support the improved quality of life of all Camden citizens.

Federal Sources

Injuries, Illnesses, and Fatalities (U.S. Bureau of Labor Statistics) - Includes tables of incidence rates and case counts for New Jersey Occupational Injuries and Illnesses from 1996 to 2000. The tables are in PDF format and require an Adobe Acrobat Reader for viewing. There is also a searchable database .

MapStats: New Jersey (FedStats)
Here you can retrieve, by state or county, statistics on a wide variety of topics, including superfund sites, births and deaths, and crime.  For more statistics see FedStats: Subjects A to Z.

U.S. Census Data
The Census Data from 2000 is available at this site.

Other Resources

American Hospital Directory - Searchable directory with free data on services provided, beds and utilization statistics, financial statistics, and inpatient and outpatient statistics.  Not all figures are available for each hospital.