| Children's Cancer & Blood FoundationEIN 13-6019222 | Health | NY | $1,119,942Small | 78.78 |
| Children's Leukemia Research AssociationEIN 11-2106778 | Health | NY | $2,362,556Small | 25.53 |
| Children's Museum of ManhattanEIN 13-2761376 | Arts, Culture, Humanities | NY | $6,228,084Mid-sized | 85.38 |
| Children's Museum of the East EndEIN 11-3431939 | Arts, Culture, Humanities | NY | $1,675,041Small | 77.02 |
| Children's RightsEIN 13-3801864 | Human Services | NY | $5,161,356Mid-sized | 81.71 |
| Children's Scholarship FundEIN 13-4002189 | Education | NY | $22,111,290Large | 89.39 |
| Children's Tumor FoundationEIN 13-2298956 | Health | NY | $12,638,073Mid-sized | 85.15 |
| China Institute in AmericaEIN 13-1623937 | International | NY | $6,411,288Mid-sized | 83.96 |
| Chofetz Chaim Heritage FoundationEIN 11-2642599 | Religion | NY | $4,420,325Mid-sized | 76.99 |
| CitiHope Relief & DevelopmentEIN 13-2907656 | International | NY | $148,169,686Large | 95.05 |
| Citizens Committee for New York CityEIN 51-0171818 | Community Development | NY | $2,613,376Small | 93.18 |
| Citizens' Committee for Children of New YorkEIN 13-5618593 | Human Services | NY | $2,913,471Small | 88.26 |
| City HarvestEIN 13-3170676 | Human Services | NY | $123,039,582Large | 87.08 |
| City Mission of SchenectadyEIN 14-1403652 | Human Services | NY | $5,157,949Mid-sized | 99.34 |
| City Parks FoundationEIN 13-3561657 | Environment | NY | $20,273,100Large | 94.26 |
| Citymeals-on-WheelsEIN 13-3634381 | Human Services | NY | $20,441,242Large | 90.36 |
| Classroom, Inc.EIN 13-3666846 | Education | NY | $4,643,853Mid-sized | 87.65 |
| Coalition Against Trafficking in WomenEIN 22-3032134 | International | NY | $720,237Small | 82.48 |
| Coalition for the HomelessEIN 13-3072967 | Human Services | NY | $11,680,807Mid-sized | 89.70 |
| Cold Spring Harbor LaboratoryEIN 11-2013303 | Research and Public Policy | NY | $147,631,524Large | 92.80 |
| Columbia/Barnard HillelEIN 23-7077182 | Religion | NY | $2,790,514Small | 75.51 |
| Columbus Citizens FoundationEIN 13-6118967 | Education | NY | $4,362,512Mid-sized | 85.20 |
| Comic Relief Inc.EIN 01-0885377 | Human Services | NY | $91,909,090Large | 89.02 |
| CommentaryEIN 13-3610041 | Arts, Culture, Humanities | NY | $3,059,126Small | 90.59 |
| Committee to Protect JournalistsEIN 13-3081500 | Human and Civil Rights | NY | $7,345,573Mid-sized | 92.83 |
| Community Foundation for Greater BuffaloEIN 22-2743917 | Community Development | NY | $24,816,523Large | 95.13 |
| Community Service Society of New YorkEIN 13-5562202 | Human Services | NY | $33,421,644Large | 91.66 |
| Community Voices Heard (CVH)EIN 13-3901997 | Community Development | NY | $1,562,711Small | 94.72 |
| Concern Worldwide US, Inc.EIN 13-3712030 | International | NY | $42,569,967Large | 90.91 |
| Concert Artists GuildEIN 13-1854253 | Arts, Culture, Humanities | NY | $1,562,144Small | 80.14 |
| Conference of Presidents of Major American Jewish Organizations FundEIN 13-3116652 | International | NY | $1,975,532Small | 77.02 |
| Coro New York Leadership CenterEIN 13-3571610 | Education | NY | $2,587,498Small | 87.70 |
| Corporation for Supportive HousingEIN 13-3600232 | Community Development | NY | $38,140,011Large | 94.67 |
| Council for Economic EducationEIN 13-1623848 | Education | NY | $5,186,704Mid-sized | 77.37 |
| Council on Foreign RelationsEIN 13-1628168 | International | NY | $69,262,800Large | 87.81 |
| Covenant House New YorkEIN 13-3076376 | Human Services | NY | $21,165,223Large | 88.04 |
| Cradle BeachEIN 16-0743025 | Human Services | NY | $2,496,471Small | 83.94 |
| Creative Capital FoundationEIN 31-1605982 | Arts, Culture, Humanities | NY | $5,792,226Mid-sized | 92.38 |
| Creative TimeEIN 13-2835847 | Arts, Culture, Humanities | NY | $2,920,073Small | 86.13 |
| Crohn's & Colitis Foundation EIN 13-6193105 | Health | NY | $75,664,404Large | 88.16 |
| CSB MinistriesEIN 36-2472249 | Religion | NY | $740,300Small | 80.96 |
| CurePSPEIN 52-1704978 | Health | NY | $2,357,223Small | 80.65 |
| Damon Runyon Cancer Research FoundationEIN 13-1933825 | Health | NY | $19,596,662Large | 94.78 |
| Dance Theatre of HarlemEIN 13-2642091 | Arts, Culture, Humanities | NY | $5,536,736Mid-sized | 83.11 |
| David Lynch Foundation for Consciousness-Based EducationEIN 83-0436453 | Education | NY | $12,365,779Mid-sized | 92.14 |
| Delivering GoodEIN 13-3300271 | Human Services | NY | $217,120,707Large | 94.69 |
| Democracy Now!EIN 01-0708733 | Arts, Culture, Humanities | NY | $7,100,320Mid-sized | 81.61 |
| DemosEIN 13-4105066 | Research and Public Policy | NY | $11,762,460Mid-sized | 87.62 |
| Dia Art FoundationEIN 23-7397946 | Arts, Culture, Humanities | NY | $16,546,314Large | 89.01 |
| DIFFAEIN 13-3224150 | Health | NY | $2,754,888Small | 79.35 |
| Diskin Orphan Fund of IsraelEIN 13-5608399 | Human Services | NY | $1,817,844Small | 75.86 |
| Do SomethingEIN 13-3720473 | Human Services | NY | $10,095,721Mid-sized | 93.37 |
| Doctors Without Borders, USAEIN 13-3433452 | International | NY | $420,595,919Large | 94.74 |
| DonorsChoose.orgEIN 13-4129457 | Education | NY | $102,666,357Large | 96.66 |
| DOROTEIN 13-3264005 | Human Services | NY | $7,626,167Mid-sized | 92.96 |
| Downtown Community Television CenterEIN 13-2742777 | Arts, Culture, Humanities | NY | $3,066,888Small | 91.45 |
| DREAMEIN 13-4025290 | Human Services | NY | $15,172,457Large | 91.42 |
| DreamYard ProjectEIN 13-3759661 | Education | NY | $5,082,563Mid-sized | 86.67 |
| Dress for Success WorldwideEIN 13-4040377 | Human Services | NY | $22,405,064Large | 91.40 |
| Drisha Institute for Jewish EducationEIN 13-2968932 | Religion | NY | $2,333,063Small | 75.76 |