| Guide Dog Foundation for the BlindEIN 11-1687477 | Animals | NY | $8,356,331Mid-sized | 89.63 |
| Guiding Eyes for the BlindEIN 13-1854606 | Animals | NY | $26,692,206Large | 86.55 |
| Guttmacher InstituteEIN 13-2890727 | Human and Civil Rights | NY | $24,621,255Large | 95.01 |
| Habitat for Humanity of Greater NewburghEIN 14-1815690 | Community Development | NY | $3,136,716Small | 92.02 |
| Habitat for Humanity of SuffolkEIN 11-2840553 | Community Development | NY | $4,199,890Mid-sized | 95.05 |
| Habitat for Humanity of WestchesterEIN 13-3522732 | Community Development | NY | $1,468,359Small | 74.70 |
| Hadassah, The Women's Zionist Organization of AmericaEIN 13-1656651 | International | NY | $84,298,455Large | 83.89 |
| Hamptons International Film FestivalEIN 11-3133786 | Arts, Culture, Humanities | NY | $1,706,012Small | 89.47 |
| Harlem AcademyEIN 56-2454573 | Education | NY | $3,672,499Mid-sized | 91.71 |
| Harlem Children's ZoneEIN 23-7112974 | Human Services | NY | $105,981,010Large | 95.19 |
| Harlem StageEIN 13-3166308 | Arts, Culture, Humanities | NY | $2,095,406Small | 68.76 |
| Harlem Village AcademiesEIN 13-4186070 | Education | NY | $5,603,763Mid-sized | 77.87 |
| HazonEIN 13-1623922 | Religion | NY | $8,812,657Mid-sized | 96.66 |
| HEAFEIN 13-3568672 | Education | NY | $2,666,102Small | 83.74 |
| HealthCare Chaplaincy NetworkEIN 13-2634080 | Religion | NY | $2,458,215Small | 89.48 |
| HealthcorpsEIN 26-1269358 | Education | NY | $3,336,435Small | 84.89 |
| HealthRight InternationalEIN 13-3791391 | International | NY | $2,425,708Small | 88.24 |
| Hearing Health FoundationEIN 13-1882107 | Health | NY | $3,570,773Mid-sized | 98.23 |
| Hebrew Free Burial AssociationEIN 13-5596755 | Religion | NY | $2,172,059Small | 91.29 |
| Hebrew Free Loan SocietyEIN 13-5562239 | Community Development | NY | $1,760,849Small | 89.65 |
| Helen Keller InternationalEIN 13-5562162 | International | NY | $75,280,180Large | 92.47 |
| Helen Keller ServicesEIN 11-1630807 | Human Services | NY | $29,871,110Large | 87.89 |
| Help From People to PeopleEIN 13-3567993 | Human Services | NY | $3,613,346Mid-sized | 85.01 |
| Henry Street SettlementEIN 13-1562242 | Human Services | NY | $36,692,652Large | 91.57 |
| Her JusticeEIN 13-3688519 | Human and Civil Rights | NY | $4,404,877Mid-sized | 89.31 |
| HEREEIN 13-3449416 | Arts, Culture, Humanities | NY | $2,145,428Small | 90.91 |
| Hereditary Disease FoundationEIN 23-7376197 | Health | NY | $2,547,618Small | 94.62 |
| Heritage for the BlindEIN 58-2164446 | Human Services | NY | $1,896,960Small | 56.15 |
| HineniEIN 11-2427999 | Religion | NY | $1,918,540Small | 71.29 |
| Hispanic FederationEIN 13-3573852 | Human Services | NY | $22,920,477Large | 93.91 |
| Holy ChildhoodEIN 16-0761224 | Human Services | NY | $9,591,850Mid-sized | 94.24 |
| HonestReporting.comEIN 06-1611859 | International | NY | $1,411,020Small | 90.54 |
| Hope & Heroes Children's Cancer FundEIN 74-3066193 | Health | NY | $2,627,367Small | 89.39 |
| Hour ChildrenEIN 13-3647412 | Human Services | NY | $4,428,790Mid-sized | 97.99 |
| Hudson Link for Higher Education in PrisonEIN 13-4132348 | Human Services | NY | $5,816,867Mid-sized | 93.91 |
| Hudson River Sloop ClearwaterEIN 14-6049022 | Environment | NY | $2,470,234Small | 81.25 |
| Human Rights FirstEIN 13-3116646 | International | NY | $11,510,302Mid-sized | 80.00 |
| Human Rights FoundationEIN 20-2669700 | International | NY | $5,323,508Mid-sized | 92.74 |
| Human Rights WatchEIN 13-2875808 | International | NY | $70,558,186Large | 85.82 |
| Humane Society of New YorkEIN 13-1624041 | Animals | NY | $5,438,620Mid-sized | 93.44 |
| Hunger Free AmericaEIN 13-3471350 | Human Services | NY | $4,119,177Mid-sized | 88.51 |
| Hunter's Hope FoundationEIN 16-1552315 | Health | NY | $868,913Small | 84.32 |
| Huntington's Disease Society of AmericaEIN 13-3349872 | Health | NY | $8,627,132Mid-sized | 92.78 |
| ICNA Relief USAEIN 04-3810161 | Human Services | NY | $14,885,429Large | 95.47 |
| iMentorEIN 30-0105507 | Education | NY | $18,667,266Large | 90.00 |
| INCLUDEnycEIN 11-2594790 | Human Services | NY | $2,915,236Small | 92.80 |
| Independent Media InstituteEIN 52-1309876 | Arts, Culture, Humanities | NY | $2,023,149Small | 77.38 |
| Inner-City Scholarship FundEIN 51-0453629 | Education | NY | $17,315,161Large | 88.90 |
| Institute for American ValuesEIN 13-3400377 | Research and Public Policy | NY | $626,271Small | 62.30 |
| Institute for Transportation and Development PolicyEIN 52-1399520 | Environment | NY | $7,664,135Mid-sized | 87.62 |
| Institute of International EducationEIN 13-1624046 | International | NY | $358,197,642Large | 83.33 |
| Institute on Religion and Public LifeEIN 52-1628303 | Research and Public Policy | NY | $2,861,837Small | 70.49 |
| International AIDS Vaccine InitiativeEIN 13-3870223 | Health | NY | $85,397,465Large | 92.92 |
| International Center of PhotographyEIN 23-7412428 | Arts, Culture, Humanities | NY | $17,276,229Large | 81.79 |
| International HouseEIN 13-1624048 | International | NY | $16,690,286Large | 88.41 |
| International Institute of Rural Reconstruction (IIRR)EIN 13-6175722 | International | NY | $4,270,136Mid-sized | 90.00 |
| International Peace InstituteEIN 03-0213226 | International | NY | $9,589,196Mid-sized | 95.34 |
| International Planned Parenthood Federation/Western Hemisphere RegionEIN 13-1845455 | Health | NY | $29,392,929Large | 93.32 |
| International Rescue CommitteeEIN 13-5660870 | International | NY | $694,099,188Large | 91.16 |
| International Senior Lawyers CorporationEIN 52-2241212 | Human and Civil Rights | NY | $1,291,304Small | 82.82 |