Since December, rabid raccoons have bitten one dog and one human. A second human was exposed when she took a raccoon to the vet for treatment.
None became sick; all received treatment.
Officials said the vaccinations are an attempt to contain the outbreak.
For one to two months beginning Tuesday, wildlife experts will begin "humanely trapping" raccoons around Central, Morningside and Riverside parks.
The animals will be vaccinated, marked for identification, and released.
The process will be repeated this summer to vaccinate raccoons born this spring.