Also, Good Shepherd School and Inwood Gourmet also suffered damage from graffiti.
A lot of the concern is focusing on the cleanup as church leaders want to get the paint off before it gets too deep into the building.
The gardens were dedicated to two dozen neighborhood people who died on 9/11.
Among them were firefighters and police officers.
"A genteleman who opens the church for us on Thanksgiving reported it to me and we alerted police," said Fr. Robert Abbatiello with Good Shepherd Church.
The vandals also tagged the gate to the parish yard outside the school.
Investigators are hoping someone notices the tag and turn people in.
The insurance will pay for the cleanup, but the church will have to pay a large deductable.
Council Member Ydanis Rodriguez released the following statement:
"I condemn in the strongest possible way the defacement of the 9/11 memorial at Good Shepherd Church. The garden memorial is a symbolic monument to the brave souls who gave their lives helping to save others on that infamous day. Therefore, this is an affront not only to the Inwood community but to the City of New York. My office has been in communication with Pastor Robert Abbatiello and expressed our desire to assist in whatever way possible. Such senseless acts of vandalism have no place in Northern Manhattan. It is utterly unacceptable and entirely uncharacteristic of what this community stands for and I expect the perpetrators to be found and punished to the fullest extent of the law."