| NEW YORK FOUNDLING | New York | P300 Human Services | $230.3M | 10 |
| American Museum of Natural History | New York | A560 Arts, Culture & Humanities | $228.7M | 17 |
| MANHATTAN COLLEGE | Riverdale | B430 Education | $226.8M | 11 |
| NEW YORK STATE TEAMSTERS COUNCIL HEALTH | Syracuse | Y43 Mutual & Membership Benefit | $224.9M | 1 |
| UNITED WELFARE FUND | New Rochelle | — | $224.5M | 6 |
| Jewish National Fund | New York | Q300 International, Foreign Affairs & National Security | $224.3M | 10 |
| TRUSTEES OF HAMILTON COLLEGE | Clinton | B420 Education | $223.9M | 16 |
| ADAPT COMMUNITY NETWORK INC | New York | G200 Diseases, Disorders & Medical Disciplines | $221.7M | 10 |
| Teach for America Inc | New York | B400 Education | $221.4M | 12 |
| CAMBA INC | Brooklyn | S20Z Community Improvement & Capacity Building | $221M | 14 |
| HITACHI AMERICA LTD HEALTH AND WELFARE | White Plains | — | $220.6M | 0 |
| JEWISH BOARD OF FAMILY & CHILDREN'S | New York | P400 Human Services | $219.6M | 13 |
| DISTRICT COUNCIL 37 HEALTH & SECURITY | New York | — | $219M | 7 |
| Northern Dutchess Hospital | Rhinebeck | E22Z Health Care | $218.4M | 12 |
| SIENA COLLEGE | Loudonville | B420 Education | $216.3M | 15 |
| PEOPLE INC | Williamsville | P82Z Human Services | $216.1M | 9 |
| UNITED FEDERATION OF TEACHERS LOCAL 2 | New York | — | $214.4M | 87 |
| CULINARY INSTITUTE OF AMERICA | Hyde Park | B30 Education | $213.8M | 14 |
| HAMASPIK CHOICE INC | Spring Valley | E92 Health Care | $212.3M | 17 |
| COMMUNITY ASSISTANCE RESOURCES & EXTENDED SERVICES INC | New York | P20 Human Services | $211.3M | 7 |
| THE FREDERICK FERRIS THOMPSON HOSPITAL | Canandaigua | E220 Health Care | $211.2M | 20 |
| CITY HARVEST INC | Brooklyn | K30Z Food, Agriculture & Nutrition | $210M | 11 |
| Rising Ground Inc | New York | P20 Human Services | $207.8M | 10 |
| INTERNATIONAL BROTHERHOOD OF TRADE | Carle Place | Y430 Mutual & Membership Benefit | $207.2M | 7 |
| HISPANIC INFORMATION AND | Brooklyn | — | $207M | 12 |
| THE GOLDMAN SACHS CHARITABLE GIFT FUND | New York | T30 Philanthropy, Voluntarism & Grantmaking Foundations | $206.6M | 0 |
| Stony Brook Internists University Faculty Practice Corporation | Stony Brook | E20 Health Care | $204.3M | 8 |
| AMALGAMATED NATIONAL HEALTH FUND | White Plains | — | $204.1M | 0 |
| GLOBAL HEALTH INVESTMENT CORPORATION | New York | E12 Health Care | $204.1M | 8 |
| THE VISITING NURSE ASSOCIATION | Syracuse | E92Z Health Care | $204M | 12 |
| CHINESE-AMERICAN PLANNING COUNCIL HOME | New York | E920 Health Care | $203.8M | 10 |
| 1199 SEIU UNITED HEALTHCARE WORKERS EAST | New York | — | $203.8M | 89 |
| ST ELIZABETH COMMUNITY HEALTH SUPPORT | Utica | E220 Health Care | $203M | 12 |
| YELED V'YALDA EARLY CHILDHOOD CENTER INC | Brooklyn | B210 Education | $202.7M | 14 |
| MERCY COLLEGE | Dobbs Ferry | B420 Education | $202.3M | 17 |
| TRUSTEES OF UNION COLLEGE IN THE TOWN OF | Schenectady | B420 Education | $201.6M | 19 |
| FEINBERG GRADUATE SCHOOL OF THE WEIZMANN INSTITUTE OF SCIENCE | New York | B500 Education | $201.3M | 10 |
| ST LAWRENCE UNIVERSITY | Canton | B42 Education | $200.6M | 14 |
| MYRIAD USA INC | New York | Q300 International, Foreign Affairs & National Security | $200.5M | 7 |
| CENTRAL PARK CONSERVANCY INC | New York | N320 Recreation & Sports | $200.2M | 13 |
| OLEAN GENERAL HOSPITAL | Olean | E220 Health Care | $199.9M | 17 |
| HUDSON HEADWATERS HEALTH NETWORK | Queensbury | E80Z Health Care | $199.7M | 13 |
| BLUE MERIDIAN PARTNERS INC | New York | P12 Human Services | $199.5M | 16 |
| THE AMERICAN UNIVERSITY IN CAIRO | New York | B43 Education | $199.1M | 13 |
| Catholic Health System | Buffalo | — | $198.1M | 20 |
| Kenmore Mercy Hospital | Buffalo | E220 Health Care | $197.1M | 21 |
| True North Medical Group PC | Westbury | E21 Health Care | $196.2M | 10 |
| YOUNG MEN'S CHRISTIAN ASSOCIATION OF | New York | P270 Human Services | $196.1M | 22 |
| DONORSCHOOSEORG | New York | B122 Education | $194M | 10 |
| URBAN HEALTH PLAN INC | Bronx | E32Z Health Care | $193.6M | 8 |
