| Literacy, Inc.EIN 13-3911331 | Education | NY | $2,604,693Small | 89.64 |
| Little Sisters of the Assumption Family Health ServiceEIN 13-2867881 | Human Services | NY | $4,959,509Mid-sized | 86.04 |
| LitWorldEIN 13-4367685 | Education | NY | $1,372,881Small | 79.95 |
| Local Initiatives Support CorporationEIN 13-3030229 | Community Development | NY | $146,056,292Large | 89.97 |
| Lollypop Farm, the Humane Society of Greater RochesterEIN 16-0743047 | Animals | NY | $7,301,943Mid-sized | 95.53 |
| Long Island Alzheimer's FoundationEIN 11-2926958 | Health | NY | $1,489,593Small | 91.39 |
| Long Island CaresEIN 11-2524512 | Human Services | NY | $14,570,325Large | 87.57 |
| Long Island Children's MuseumEIN 11-3035221 | Arts, Culture, Humanities | NY | $4,693,196Mid-sized | 82.81 |
| Long Island Council on Alcoholism & Drug DependenceEIN 11-1833092 | Health | NY | $1,457,603Small | 83.38 |
| Lower Manhattan Cultural CouncilEIN 23-7348782 | Arts, Culture, Humanities | NY | $3,660,793Mid-sized | 87.43 |
| LumberyardEIN 52-2158599 | Arts, Culture, Humanities | NY | $5,356,697Mid-sized | 84.71 |
| Lung Cancer Research FoundationEIN 14-1935776 | Health | NY | $4,554,246Mid-sized | 92.20 |
| Lupus Research AllianceEIN 58-2492929 | Health | NY | $28,260,250Large | 91.47 |
| Lymphoma Research FoundationEIN 95-4335088 | Health | NY | $8,784,268Mid-sized | 79.06 |
| Madison Square Boys & Girls ClubEIN 13-5596792 | Human Services | NY | $10,016,984Mid-sized | 92.12 |
| Madison Square Park ConservancyEIN 14-1859935 | Environment | NY | $4,811,212Mid-sized | 85.67 |
| MADREEIN 13-3280194 | International | NY | $4,284,836Mid-sized | 95.83 |
| Make the Road New YorkEIN 11-3344389 | Human and Civil Rights | NY | $16,758,025Large | 86.98 |
| Make-A-Wish Foundation of Central New YorkEIN 22-2572086 | Health | NY | $1,700,156Small | 74.64 |
| Make-A-Wish Foundation of Metro New York and Western New YorkEIN 11-2645641 | Health | NY | $13,532,441Large | 84.57 |
| Make-A-Wish Foundation of Northeast New YorkEIN 14-1703503 | Health | NY | $2,120,871Small | 86.06 |
| Make-A-Wish Foundation of Suffolk County, NYEIN 11-2666969 | Health | NY | $1,706,107Small | 90.47 |
| Make-A-Wish Foundation of the Hudson ValleyEIN 13-3344306 | Health | NY | $2,644,291Small | 82.30 |
| Manhattan Institute for Policy ResearchEIN 13-2912529 | Research and Public Policy | NY | $18,832,278Large | 94.25 |
| Manhattan Theatre ClubEIN 23-7086643 | Arts, Culture, Humanities | NY | $27,356,114Large | 90.34 |
| Mark Morris Dance GroupEIN 13-3577394 | Arts, Culture, Humanities | NY | $8,923,444Mid-sized | 91.94 |
| MasbiaEIN 20-1923521 | Human Services | NY | $1,581,255Small | 67.39 |
| Masonic Medical Research LaboratoryEIN 13-5648611 | Health | NY | $3,253,665Small | 79.52 |
| MasterVoicesEIN 13-1606158 | Arts, Culture, Humanities | NY | $1,780,240Small | 86.08 |
| Mayor's Alliance for NYC's AnimalsEIN 73-1653635 | Animals | NY | $1,632,234Small | 76.21 |
| Mayor's Fund to Advance New York CityEIN 13-3783906 | Community Development | NY | $22,870,687Large | 87.30 |
| MCC TheaterEIN 13-3391844 | Arts, Culture, Humanities | NY | $5,134,774Mid-sized | 86.29 |
| Meals on Wheels Programs & Services of Rockland, Inc.EIN 13-2831197 | Human Services | NY | $3,338,475Small | 84.15 |
| Medical Development for IsraelEIN 13-3140298 | Health | NY | $531,029Small | 68.38 |
| Medicare Rights CenterEIN 13-3505372 | Human and Civil Rights | NY | $3,721,313Mid-sized | 91.45 |
| Mental Health AssociationEIN 16-1395575 | Health | NY | $2,486,317Small | 89.45 |
| MEOREIN 51-0430002 | Religion | NY | $6,140,357Mid-sized | 78.94 |
| Mercy Flight CentralEIN 16-1427751 | Health | NY | $8,551,804Mid-sized | 83.72 |
| Mesorah Heritage FoundationEIN 11-2981112 | Religion | NY | $8,542,211Mid-sized | 84.50 |
| Metropolitan Museum of ArtEIN 13-1624086 | Arts, Culture, Humanities | NY | $492,173,112Large | 95.80 |
| Michael J. Fox Foundation for Parkinson's ResearchEIN 13-4141945 | Health | NY | $112,000,466Large | 92.92 |
| Midori & FriendsEIN 13-3682472 | Education | NY | $1,764,343Small | 91.24 |
| Millennium PromiseEIN 20-3042135 | International | NY | $15,047,799Large | 77.83 |
| Mint Theater CompanyEIN 13-3687725 | Arts, Culture, Humanities | NY | $1,894,443Small | 90.96 |
| MisaskimEIN 20-3957164 | Religion | NY | $1,776,940Small | 59.99 |
| Modest NeedsEIN 47-0863430 | Human Services | NY | $1,226,134Small | 83.84 |
| Mohawk Hudson Humane SocietyEIN 14-1338459 | Animals | NY | $3,033,879Small | 88.69 |
| Mohonk PreserveEIN 14-1609484 | Environment | NY | $4,259,553Mid-sized | 81.21 |
| MoMA PS1EIN 23-7379091 | Arts, Culture, Humanities | NY | $9,938,950Mid-sized | 82.27 |
| MouseEIN 13-3973196 | Education | NY | $2,010,423Small | 94.27 |
| Moving Picture InstituteEIN 20-3237801 | Arts, Culture, Humanities | NY | $3,489,969Small | 97.87 |
| Ms. Foundation for WomenEIN 23-7252609 | Human and Civil Rights | NY | $7,138,935Mid-sized | 79.00 |
| Multiplying GoodEIN 52-0959336 | Education | NY | $2,882,955Small | 83.75 |
| Museum at Eldridge StreetEIN 13-3379555 | Arts, Culture, Humanities | NY | $1,386,823Small | 86.45 |
| Museum of American FinanceEIN 13-3540880 | Arts, Culture, Humanities | NY | $4,447,277Mid-sized | 78.86 |
| Museum of Arts & DesignEIN 13-3585408 | Arts, Culture, Humanities | NY | $12,077,991Mid-sized | 83.32 |
| Museum of the City of New YorkEIN 13-1624098 | Arts, Culture, Humanities | NY | $21,990,267Large | 93.58 |
| Museum of the Moving ImageEIN 11-2730714 | Arts, Culture, Humanities | NY | $6,904,332Mid-sized | 83.07 |
| Music Conservatory of WestchesterEIN 13-6007082 | Education | NY | $2,941,062Small | 76.63 |
| myFaceEIN 13-6013760 | Health | NY | $3,618,719Mid-sized | 91.74 |