| NEW YORK INSTITUTE OF TECHNOLOGY | Old Westbury | B430 Education | $352.2M | 14 |
| THE OJC FUND | Brooklyn | B90 Education | $350.7M | 2 |
| COLGATE UNIVERSITY | Hamilton | B42Z Education | $350M | 18 |
| SAMARITAN MEDICAL CENTER | Watertown | E220 Health Care | $349.2M | 19 |
| ST JOHNS RIVERSIDE HOSPITAL | Yonkers | E220 Health Care | $347.2M | 17 |
| Wildlife Conservation Society | Bronx | D500 Animal-Related | $345.5M | 15 |
| ADELPHI UNIVERSITY | Garden City | B430 Education | $344.3M | 17 |
| Central Suffolk Hospital | Westbury | E220 Health Care | $339.7M | 21 |
| CAYUGA MEDICAL CENTER AT ITHACA | Ithaca | E220 Health Care | $338.3M | 23 |
| PRATT INSTITUTE | Brooklyn | B430 Education | $337.7M | 14 |
| MARSH & MCLENNAN COMPANIES ER | New York | — | $336.8M | 1 |
| PARTNERS HEALTH PLAN INC | Bronx | E800 Health Care | $336.5M | 7 |
| CHS SERVICES INC | Rockville Centre | — | $334.3M | 7 |
| Acacia Network Housing Inc | Bronx | L41 Housing & Shelter | $333.4M | 10 |
| MARIST COLLEGE | Poughkeepsie | B430 Education | $333M | 18 |
| THE MENTAL HEALTH ASSOCIATION OF NEW YORK | New York | — | $332.4M | 9 |
| THE PETER AND CARMEN LUCIA BUCK | New York | T20 Philanthropy, Voluntarism & Grantmaking Foundations | $331.4M | 7 |
| CARNEGIE CORPORATION OF NEW YORK | New York | B124 Education | $330.1M | 12 |
| FUND FOR POLICY REFORM INC | New York | W05 Public & Societal Benefit | $329.1M | 7 |
| CL HEALTHCARE INC | Flushing | X99 Religion-Related | $329M | 11 |
| SRC Inc | North Syracuse | Z99 Unknown | $326.5M | 27 |
| CATHOLIC MEDICAL MISSION BOARD INC | Long Island City | Q300 International, Foreign Affairs & National Security | $324.3M | 7 |
| THE JPB FOUNDATION | New York | T21 Philanthropy, Voluntarism & Grantmaking Foundations | $323.9M | 4 |
| HEALTH SCIENCE CENTER AT BROOKLYN | Brooklyn | B5BI Education | $321.5M | 17 |
| MERCY MEDICAL CENTER | Rockville Centre | E220 Health Care | $320M | 11 |
| HAMASPIK CARE INC | Spring Valley | E92 Health Care | $318.6M | 8 |
| EXCAVATORS UNION 731 WELFARE | Astoria | — | $317.8M | 8 |
| HUDSON VALLEY CREDIT UNION | Poughkeepsie | W61 Public & Societal Benefit | $314.7M | 15 |
| SAMARITAN DAYTOP VILLAGE INC | Briarwood | F220 Mental Health & Crisis Intervention | $313.7M | 10 |
| BARNARD COLLEGE | New York | B420 Education | $313.7M | 17 |
| DISTRICT COUNCIL 37 BENEFITS FUND TRUST | New York | — | $313M | 5 |
| AMIDA CARE INC | New York | E31 Health Care | $311.4M | 9 |
| IATSE NATIONAL HEALTH AND WELFARE | New York | — | $309.5M | 6 |
| NYSARC INC NEW YORK CITY CHAPTER | New York | P820 Human Services | $308.1M | 9 |
| ST JOSEPH'S HOSPITAL YONKERS | Yonkers | E220 Health Care | $304M | 13 |
| BARD COLLEGE | Annandaleonhudson | B43Z Education | $304M | 12 |
| PLAINVIEW HOSPITAL | Westbury | E20 Health Care | $299.5M | 20 |
| ENVIRONMENTAL DEFENSE FUND INCORPORATED | New York | C600 Environment | $298.7M | 13 |
| SUN RIVER HEALTH INC | Peekskill | E320 Health Care | $296.6M | 10 |
| CAPITAL AREA SCHOOLS HEALTH | Scotia | — | $295.8M | 0 |
| HUDSON VALLEY HOSPITAL CENTER | Cortlandt Manor | E220 Health Care | $295.6M | 20 |
| SKIDMORE COLLEGE | Saratoga Springs | B420 Education | $292.6M | 21 |
| ALBANY MED HEALTH SYSTEM | Albany | E21 Health Care | $292.6M | 14 |
| NATIONAL BASKETBALL PLAYERS ASSOCIATION | New York | — | $291M | 9 |
| RF CATALYTIC CAPITAL INC | New York | T30 Philanthropy, Voluntarism & Grantmaking Foundations | $289M | 10 |
| NEW YORK STATE INDUSTRIES | Albany | — | $288.9M | 6 |
| SB Clinical Practice Management Plan Inc | Stony Brook | E99 Health Care | $288.3M | 28 |
| DUTCHESS EDUCATIONAL HEALTH INSURANCE | Poughkeepsie | — | $288.2M | 0 |
| KINGS PHYSICIAN SERVICES PC | Brooklyn | E20 Health Care | $286.9M | 6 |
| VASSAR COLLEGE | Poughkeepsie | — | $284.4M | 17 |
