| Drug Policy AllianceEIN 52-1516692 | Research and Public Policy | NY | $14,612,498Large | 76.86 |
| Drugs for Neglected Diseases Initiative North AmericaEIN 20-8774179 | Health | NY | $4,091,229Mid-sized | 84.44 |
| Dutchess County SPCAEIN 14-1340058 | Animals | NY | $2,016,618Small | 85.23 |
| Dysautonomia FoundationEIN 13-6145280 | Health | NY | $2,427,386Small | 85.38 |
| Dystrophic Epidermolysis Bullosa Research Association of America (debra of America)EIN 11-2519726 | Health | NY | $1,416,573Small | 93.82 |
| East Harlem Tutorial ProgramEIN 23-7439789 | Education | NY | $9,065,798Mid-sized | 92.30 |
| East Side HouseEIN 13-1623989 | Human Services | NY | $22,000,963Large | 98.23 |
| EastWest InstituteEIN 13-3091844 | International | NY | $8,643,444Mid-sized | 91.02 |
| EcoHealth AllianceEIN 31-1726494 | Animals | NY | $13,652,783Large | 92.92 |
| Edith and Carl Marks Jewish Community House of BensonhurstEIN 11-1633484 | Human Services | NY | $9,407,466Mid-sized | 91.97 |
| Education Through Music, Inc. (New York)EIN 13-3613210 | Education | NY | $4,975,061Mid-sized | 93.96 |
| EFRAT-C.R.I.B. Committee for the Rescue of Israel's BabiesEIN 22-3431457 | Human Services | NY | $2,588,353Small | 86.13 |
| El Museo del BarrioEIN 23-7156720 | Arts, Culture, Humanities | NY | $3,296,157Small | 74.33 |
| ELEM/Youth in Distress in IsraelEIN 13-3171815 | Human Services | NY | $888,375Small | 74.55 |
| Elie Wiesel Foundation for HumanityEIN 13-3398151 | International | NY | $1,039,897Small | 80.59 |
| Elton John AIDS FoundationEIN 58-2033460 | Health | NY | $10,028,552Mid-sized | 95.12 |
| EMpowerEIN 03-0529005 | International | NY | $4,505,664Mid-sized | 91.55 |
| Emunah of AmericaEIN 13-2670365 | Human Services | NY | $5,123,297Mid-sized | 82.55 |
| enCourage Kids FoundationEIN 13-3442216 | Health | NY | $3,110,680Small | 89.25 |
| EndeavorEIN 13-3931449 | International | NY | $9,653,170Mid-sized | 89.63 |
| Environmental Advocates of New YorkEIN 22-2360736 | Environment | NY | $1,251,586Small | 99.79 |
| Environmental Grantmakers AssociationEIN 20-8817646 | Environment | NY | $2,539,563Small | 91.44 |
| Episcopal Charities of the Diocese of New YorkEIN 13-3902908 | Human Services | NY | $1,785,346Small | 86.42 |
| Episcopal Church FoundationEIN 13-1776448 | Religion | NY | $4,278,329Mid-sized | 86.61 |
| Episcopal Relief & DevelopmentEIN 73-1635264 | International | NY | $21,968,901Large | 91.01 |
| Equality NowEIN 13-3660566 | International | NY | $4,916,223Mid-sized | 94.13 |
| Equine AdvocatesEIN 11-3313534 | Animals | NY | $1,445,721Small | 87.52 |
| Everytown for Gun Safety Support FundEIN 26-1598353 | Research and Public Policy | NY | $15,515,941Large | 76.39 |
| Exploring the ArtsEIN 13-4069251 | Education | NY | $2,017,353Small | 85.17 |
| Eye to EyeEIN 51-0570498 | Education | NY | $2,776,402Small | 96.18 |
| EyebeamEIN 13-3952075 | Arts, Culture, Humanities | NY | $1,057,256Small | 73.66 |
| Ezer MizionEIN 13-3660421 | Health | NY | $3,532,701Mid-sized | 80.91 |
| Ezras TorahEIN 13-5562218 | International | NY | $1,466,996Small | 64.20 |
| FACE FoundationEIN 13-6165672 | International | NY | $2,861,348Small | 75.38 |
| Family Equality CouncilEIN 52-1438455 | Human and Civil Rights | NY | $2,186,108Small | 72.01 |
| Family Life MinistriesEIN 16-0863914 | Religion | NY | $5,301,288Mid-sized | 95.64 |
| Farm SanctuaryEIN 51-0292919 | Animals | NY | $11,633,460Mid-sized | 88.58 |
| Fashion Institute of Technology FoundationEIN 13-5675757 | Education | NY | $5,704,618Mid-sized | 82.99 |
| Fatima NetworkEIN 22-2396744 | Religion | NY | $3,766,074Mid-sized | 80.97 |
| FDNY FoundationEIN 11-2632404 | Human Services | NY | $7,326,345Mid-sized | 98.23 |
| Federation of Protestant Welfare AgenciesEIN 13-5562220 | Human Services | NY | $7,188,669Mid-sized | 87.19 |
| Feeding WestchesterEIN 13-3507988 | Human Services | NY | $13,681,006Large | 87.34 |
| Fifth Avenue CommitteeEIN 11-2475743 | Community Development | NY | $5,978,755Mid-sized | 85.83 |
| Figure Skating in HarlemEIN 13-3945168 | Human Services | NY | $2,243,344Small | 88.38 |
| Film ForumEIN 51-0175953 | Arts, Culture, Humanities | NY | $5,491,172Mid-sized | 86.89 |
| Film Society of Lincoln CenterEIN 23-7042553 | Arts, Culture, Humanities | NY | $14,711,616Large | 94.45 |
| Firefighters Charitable FoundationEIN 65-0258322 | Human Services | NY | $7,204,428Mid-sized | 28.86 |
| Fisher Center for Alzheimer's Research FoundationEIN 13-3859563 | Health | NY | $4,628,453Mid-sized | 100.00 |
| Fiver Children's FoundationEIN 13-3993633 | Human Services | NY | $1,900,994Small | 94.62 |
| FJCEIN 13-3848582 | Community Development | NY | $38,216,328Large | 93.69 |
| Flatbush Volunteers of HatzolohEIN 13-3213138 | Health | NY | $1,354,561Small | 73.69 |
| Flower City Habitat for HumanityEIN 13-3281487 | Community Development | NY | $3,003,163Small | 90.97 |
| Folksbiene Yiddish TheatreEIN 13-3998872 | Arts, Culture, Humanities | NY | $1,798,228Small | 73.19 |
| Food Bank For New York CityEIN 13-3179546 | Human Services | NY | $82,139,683Large | 80.56 |
| Food Bank of Central New YorkEIN 22-2816988 | Human Services | NY | $26,000,869Large | 91.23 |
| Food Bank of Western New York, Inc.EIN 22-2470820 | Human Services | NY | $24,290,667Large | 93.16 |
| FoodlinkEIN 22-2428304 | Human Services | NY | $33,287,225Large | 89.00 |
| Foreign Policy AssociationEIN 13-1624007 | International | NY | $4,126,892Mid-sized | 85.08 |
| Fort Ticonderoga AssociationEIN 14-1440924 | Arts, Culture, Humanities | NY | $3,442,794Small | 94.39 |
| Foundation for Contemporary ArtsEIN 13-1978163 | Arts, Culture, Humanities | NY | $1,919,759Small | 88.67 |