| AMERICAN FRIENDS OF MAGEN DAVID ADOM | New York | Q113 International, Foreign Affairs & National Security | $142.3M | 11 |
| GRAMEEN AMERICA INC | Jackson Heights | S31 Community Improvement & Capacity Building | $141.8M | 11 |
| USTA NATIONAL TENNIS CENTER INCORPORATED | Purchase | N660 Recreation & Sports | $140.8M | 7 |
| NEIGHBORHOOD ASSOCIATION FOR INTERCULTURAL AFFAIRS INC | Bronx | — | $140.5M | 16 |
| CLIFTON SPRINGS SANITARIUM CO | Clifton Springs | E22 Health Care | $140.3M | 16 |
| WORLD EDUCATION SERVICES INC | New York | Q22Z International, Foreign Affairs & National Security | $139.6M | 13 |
| ASCEND CHARTER SCHOOLS | Brooklyn | B29 Education | $139.3M | 9 |
| LOCAL 804 WELFARE TRUST FUND | Port Washington | — | $138.8M | 11 |
| ST BONAVENTURE UNIVERSITY | St Bonaventure | — | $138.7M | 15 |
| TNTP INC | New York | B90 Education | $138.6M | 14 |
| WMC-New York Inc | Valhalla | E20 Health Care | $138.4M | 8 |
| SARAH LAWRENCE COLLEGE | Bronxville | B420 Education | $138.4M | 12 |
| WNET | New York | A32 Arts, Culture & Humanities | $138.4M | 15 |
| CATHOLIC HEALTH SYSTEM OF LONG ISLAND | Rockville Centre | — | $138.3M | 10 |
| ST JOSEPH'S UNIVERSITY NEW YORK | Brooklyn | B420 Education | $138M | 20 |
| WELLLIFE NETWORK INC | New Hyde Park | P820 Human Services | $137M | 7 |
| THE AMERICAN SOCIETY OF MECHANICAL ENGINEERS | New York | U030 Science & Technology | $136.7M | 11 |
| ALFRED UNIVERSITY | Alfred | B430 Education | $136.3M | 13 |
| AMDA INC (AMERICAN MUSICAL AND DRAMATIC ACADEMY) | New York | — | $135.5M | 9 |
| DELIVERING GOOD INC | New York | P190 Human Services | $135.5M | 5 |
| EQUITABLE FACILITIES FUND INC | New York | B11 Education | $134.9M | 7 |
| CENTER FOR EMPLOYMENT OPPORTUNITIES INC | New York | J20 Employment | $134M | 8 |
| CENTER FOR INTERNET SECURITY INC | East Greenbush | W50 Public & Societal Benefit | $132.8M | 24 |
| NEW YORK ROAD RUNNERS INC C/O FINANCE DEPARTMENT | New York | — | $132.7M | 8 |
| VITAL STRATEGIES INC | New York | Q30 International, Foreign Affairs & National Security | $132.4M | 15 |
| WESTERN NEW YORK MEDICAL PRACTICE PC | Rochester | E300 Health Care | $132.2M | 6 |
| CARE DESIGN NY LLC | Albany | E86 Health Care | $131.5M | 17 |
| COMMUNITY HEALTH PROJECT INC | New York | E32Z Health Care | $131.5M | 10 |
| Service Employees International Union Local 32BJ | New York | — | $131.2M | 132 |
| INTERNATIONAL AIDS VACCINE INITIATIVE INC | New York | Q300 International, Foreign Affairs & National Security | $131.2M | 11 |
| ST MARYS HOSPITAL FOR CHILDREN INC | Bayside | E240 Health Care | $130.5M | 13 |
| UNIVERSITY OF MOUNT SAINT VINCENT | Riverdale | B420 Education | $130.3M | 8 |
| CALVARY HOSPITAL INC | Bronx | E240 Health Care | $129.8M | 14 |
| BROOKLYN NAVY YARD DEVELOPMENT CORP | Brooklyn | S200 Community Improvement & Capacity Building | $129.6M | 18 |
| BRAVERHOOD LTD | Brooklyn | B990 Education | $129.5M | 9 |
| ETHICAL CULTURE FIELDSTON SCHOOL | New York | B200 Education | $129.3M | 25 |
| LOCAL 282 WELFARE TRUST FUND | Lake Success | — | $128.3M | 6 |
| Heartshare Human Services of New York | Brooklyn | P200 Human Services | $128.1M | 9 |
| HELP USA INC AND AFFILIATES | New York | L410 Housing & Shelter | $127.9M | 16 |
| BRONXWORKS INC | Bronx | P200 Human Services | $127.6M | 10 |
| THE YOUNG MEN'S AND YOUNG WOMEN'S HEBREW ASSOCIATION | New York | X110 Religion-Related | $127.6M | 13 |
| SUE & EDGAR WACHENHEIM FOUNDATION | Purchase | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $127.2M | 0 |
| STEPHEN A SCHWARZMAN FOUNDATION | New York | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $127.1M | 2 |
| INDEPENDENT SUPPORT SERVICES INC | Monticello | F30 Mental Health & Crisis Intervention | $127M | 4 |
| THE BRONX PARENT HOUSING NETWORK INC | Bronx | P80 Human Services | $126.4M | 8 |
| NAZARETH UNIVERSITY | Rochester | B420 Education | $126.3M | 15 |
| ITHAKA HARBORS INC | New York | V30 Social Science | $126M | 24 |
| ELIZABETH SETON PEDIATRIC CENTER | Yonkers | — | $125.9M | 8 |
| CENTER FOR DISABILITY SERVICESINC | Albany | G200 Diseases, Disorders & Medical Disciplines | $125.8M | 8 |
| GOOD SHEPHERD SERVICES | New York | P20 Human Services | $125.4M | 7 |
