| Wildlife Conservation Society | Bronx | D500 Animal-Related | $389.2M | 15 |
| THE OJC FUND | Brooklyn | B90 Education | $386.6M | 2 |
| CANTON-POTSDAM HOSPITAL | Potsdam | E22Z Health Care | $385.7M | 14 |
| THE LEONA M AND HARRY B HELMSLEY CHARITABLE TRUST | New York | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $385.2M | 8 |
| TOURO UNIVERSITY | New York | B420 Education | $382.7M | 20 |
| NEW YORK INSTITUTE OF TECHNOLOGY | Old Westbury | B430 Education | $381.5M | 14 |
| MARIST UNIVERSITY | Poughkeepsie | B430 Education | $379.5M | 18 |
| Montefiore Nyack Hospital | Nyack | E220 Health Care | $378M | 11 |
| SAMARITAN MEDICAL CENTER | Watertown | E220 Health Care | $376.6M | 21 |
| NEW YORK-PRESBYTERIAN FUND INC | New York | E120 Health Care | $375.5M | 12 |
| STEPHEN SILLER TUNNEL TO TOWERS FOUNDATION | Staten Island | B82 Education | $373M | 0 |
| LONG ISLAND COMMUNITY HOSPITAL AT NYU LANGONE HEALTH | Patchogue | E220 Health Care | $370M | 16 |
| ITHACA COLLEGE | Ithaca | B420 Education | $369.6M | 28 |
| LOCAL INITIATIVES SUPPORT CORPORATION | New York | S200 Community Improvement & Capacity Building | $363.9M | 54 |
| CATHOLIC MANAGED LONG TERM CARE INC | New York | E60 Health Care | $358.4M | 8 |
| PHYSICIANS OF UNIVERSITY HOSPITAL PC | Westbury | E30 Health Care | $356.3M | 11 |
| Nuvance Health | Poughkeepsie | E11 Health Care | $352.8M | 16 |
| BARNARD COLLEGE | New York | B420 Education | $351.5M | 19 |
| CHS SERVICES INC | Rockville Centre | — | $350.8M | 7 |
| Acacia Network Housing Inc | Bronx | L41 Housing & Shelter | $347.4M | 11 |
| ST JOHNS RIVERSIDE HOSPITAL ANDRUS PARKCARE & DOBBS FERRY | Yonkers | E220 Health Care | $347.2M | 17 |
| ADELPHI UNIVERSITY | Garden City | B430 Education | $344.3M | 17 |
| Central Suffolk Hospital C/O NORTHWELL HEALTH INC | Westbury | E220 Health Care | $339.7M | 21 |
| SAMARITAN DAYTOP VILLAGE INC | Briarwood | F220 Mental Health & Crisis Intervention | $338.9M | 10 |
| MARSH & MCLENNAN COMPANIES ER FUNDED WELFARE BENEFITS TRUST | New York | — | $336.8M | 1 |
| CL HEALTHCARE INC | Flushing | X99 Religion-Related | $336.7M | 10 |
| PARTNERS HEALTH PLAN INC | Bronx | E800 Health Care | $336.5M | 7 |
| MERCY MEDICAL CENTER | Rockville Centre | E220 Health Care | $333M | 10 |
| BARD COLLEGE | Annandaleonhudson | B43Z Education | $331.9M | 12 |
| THE PETER AND CARMEN LUCIA BUCK FOUNDATION INC | New York | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $331.4M | 7 |
| CARNEGIE CORPORATION OF NEW YORK | New York | B124 Education | $330.1M | 12 |
| WELLSPRING PHILANTHROPIC FUND INC | New York | T22 Philanthropy, Voluntarism & Grantmaking Foundations | $329.3M | 4 |
| VASSAR COLLEGE | Poughkeepsie | — | $327.5M | 18 |
| SRC Inc | North Syracuse | Z99 Unknown | $326.5M | 27 |
| NYSARC INC NEW YORK CITY CHAPTER | New York | P820 Human Services | $326.4M | 9 |
| Museum of Modern Art | New York | A510 Arts, Culture & Humanities | $324.7M | 22 |
| CATHOLIC MEDICAL MISSION BOARD INC | Long Island City | Q300 International, Foreign Affairs & National Security | $324.3M | 7 |
| THE MENTAL HEALTH ASSOCIATION OF NEW YORK CITY INC | New York | — | $324.1M | 10 |
| THE NEW YORK COMMUNITY TRUST | New York | T310 Philanthropy, Voluntarism & Grantmaking Foundations | $322.6M | 17 |
| HEALTH SCIENCE CENTER AT BROOKLYN FOUNDATION | Brooklyn | B5BI Education | $321.5M | 17 |
| HAMASPIK CARE INC | Spring Valley | E92 Health Care | $318.6M | 8 |
| EXCAVATORS UNION 731 WELFARE | Astoria | — | $317.8M | 8 |
| DISTRICT COUNCIL 37 BENEFITS FUND TRUST | New York | — | $313M | 5 |
| AMIDA CARE INC | New York | E31 Health Care | $311.4M | 9 |
| WEILL CORNELL IMAGING AT NEWYORK-PRESBYTERIAN | New York | E60 Health Care | $308.2M | 10 |
| CHS PHYSICIAN PARTNERS PC | Roslyn | E31 Health Care | $307.9M | 4 |
| KINGS PHYSICIAN SERVICES PC | Brooklyn | E20 Health Care | $307.3M | 6 |
| AMERICAN CIVIL LIBERTIES UNION FOUNDATION INC | New York | R600 Civil Rights, Social Action & Advocacy | $306.8M | 16 |
| ST JOSEPH'S HOSPITAL YONKERS | Yonkers | E220 Health Care | $304M | 13 |
| BRYANT & STRATTON COLLEGE INC | Orchard Park | B40 Education | $302.4M | 17 |
