| Seneca Park Zoo SocietyEIN 16-0905390 | Animals | NY | $5,429,091Mid-sized | 81.24 |
| Sephardic Food Fund EIN 56-2307777 | Human Services | NY | $2,663,245Small | 61.26 |
| SHAREEIN 13-3131914 | Health | NY | $1,754,882Small | 91.66 |
| Shared InterestEIN 13-3836581 | International | NY | $2,086,363Small | 89.75 |
| Single Stop USAEIN 20-8837690 | Human Services | NY | $21,924,829Large | 80.68 |
| Skin Cancer FoundationEIN 13-2948778 | Health | NY | $4,550,855Mid-sized | 92.38 |
| Society for Classical StudiesEIN 13-6018127 | Education | NY | $1,277,954Small | 93.82 |
| SoliyaEIN 32-0060209 | International | NY | $1,365,656Small | 72.22 |
| Solomon R. Guggenheim FoundationEIN 13-5562233 | Arts, Culture, Humanities | NY | $80,072,379Large | 78.32 |
| South Asian Youth ActionEIN 13-3943630 | Human Services | NY | $3,370,395Small | 95.04 |
| South Street Seaport MuseumEIN 13-2596500 | Arts, Culture, Humanities | NY | $3,179,707Small | 82.13 |
| SPCA InternationalEIN 87-0773320 | Animals | NY | $14,673,812Large | 72.62 |
| SPCA of WestchesterEIN 13-1740069 | Animals | NY | $2,832,609Small | 100.00 |
| SPCA Serving Erie CountyEIN 16-0425315 | Animals | NY | $6,268,446Mid-sized | 86.67 |
| Spence-Chapin Services to Families and ChildrenEIN 13-1834590 | Human Services | NY | $7,266,046Mid-sized | 81.35 |
| Sponsors for Educational Opportunity (SEO)EIN 13-2578670 | Education | NY | $17,839,508Large | 99.93 |
| St. John's Bread & LifeEIN 11-3174514 | Human Services | NY | $4,064,642Mid-sized | 89.71 |
| Stanley M. Isaacs Neighborhood CenterEIN 13-2572034 | Human Services | NY | $7,899,036Mid-sized | 86.21 |
| State University College at Oneonta Foundation CorporationEIN 22-2403203 | Education | NY | $3,696,700Mid-sized | 92.96 |
| Staten Island Economic Development Corporation (SIEDC)EIN 13-3706442 | Community Development | NY | $1,787,552Small | 86.03 |
| Statue of Liberty-Ellis Island FoundationEIN 13-3118415 | Arts, Culture, Humanities | NY | $18,817,780Large | 92.24 |
| Stephen Siller Tunnel to Towers FoundationEIN 02-0554654 | Human Services | NY | $16,641,583Large | 98.23 |
| Stevens-Swan Humane Society of Oneida CountyEIN 15-0551485 | Animals | NY | $1,087,872Small | 77.21 |
| Storefront Academy HarlemEIN 13-2940671 | Education | NY | $3,785,092Mid-sized | 79.48 |
| Storm King Art CenterEIN 14-1457573 | Arts, Culture, Humanities | NY | $8,396,023Mid-sized | 89.00 |
| StoryCorpsEIN 13-3753011 | Arts, Culture, Humanities | NY | $10,638,243Mid-sized | 94.93 |
| STRIVEEIN 13-3255679 | Human Services | NY | $6,254,660Mid-sized | 88.95 |
| Student Leadership NetworkEIN 06-1517218 | Education | NY | $9,472,942Mid-sized | 92.02 |
| Student Sponsor PartnersEIN 13-3392965 | Education | NY | $7,283,038Mid-sized | 91.46 |
| Studio in a SchoolEIN 13-3003112 | Education | NY | $6,718,983Mid-sized | 88.27 |
| Studio Museum in HarlemEIN 13-2590805 | Arts, Culture, Humanities | NY | $7,761,083Mid-sized | 88.58 |
| Suffolk County Police Athletic LeagueEIN 23-7356002 | Human Services | NY | $1,095,091Small | 76.76 |
| Summer Camp Opportunities Promote Education (SCOPE)EIN 20-2772242 | Education | NY | $713,151Small | 72.80 |
| Supportive Housing Network of New YorkEIN 13-3755149 | Research and Public Policy | NY | $1,876,483Small | 87.00 |
| Symphony SpaceEIN 13-2941455 | Arts, Culture, Humanities | NY | $6,686,548Mid-sized | 91.83 |
| SynergosEIN 13-3392006 | International | NY | $14,088,067Large | 93.42 |
| Syracuse StageEIN 15-0623468 | Arts, Culture, Humanities | NY | $5,682,361Mid-sized | 84.78 |
| T.J. Martell FoundationEIN 51-0180178 | Health | NY | $2,895,000Small | 83.37 |
| Tada! Youth TheaterEIN 13-3311294 | Education | NY | $1,900,387Small | 70.86 |
| Tanenbaum Center for Interreligious UnderstandingEIN 13-3695475 | Research and Public Policy | NY | $1,992,629Small | 90.41 |
| TB AllianceEIN 13-4128413 | Health | NY | $54,033,661Large | 95.64 |
| Teach For AmericaEIN 13-3541913 | Education | NY | $287,132,584Large | 88.00 |
| Teaching MattersEIN 13-3770472 | Education | NY | $6,009,669Mid-sized | 94.45 |
| The 52nd Street ProjectEIN 13-3467948 | Human Services | NY | $2,060,817Small | 91.70 |
| The 92nd Street YEIN 13-1624229 | Human Services | NY | $69,602,246Large | 88.59 |
| The Abraham Fund InitiativesEIN 13-3556715 | International | NY | $1,446,990Small | 81.05 |
| The Acting CompanyEIN 13-2759292 | Arts, Culture, Humanities | NY | $2,167,703Small | 76.11 |
| The Actors FundEIN 13-1635251 | Arts, Culture, Humanities | NY | $34,504,429Large | 92.52 |
| The Adirondack CouncilEIN 14-1594386 | Environment | NY | $1,901,232Small | 97.45 |
| The ALS Association Greater New York ChapterEIN 13-3616680 | Health | NY | $5,132,118Mid-sized | 97.66 |
| The American Committee for the Tel Aviv FoundationEIN 13-3145161 | International | NY | $3,796,330Mid-sized | 89.50 |
| The Animal Medical CenterEIN 13-5505367 | Animals | NY | $47,432,319Large | 87.71 |
| The Armory FoundationEIN 13-3680286 | Human Services | NY | $6,815,239Mid-sized | 94.66 |
| The Avon FoundationEIN 13-6128447 | Health | NY | $9,254,623Mid-sized | 72.73 |
| The Battery ConservancyEIN 13-3769101 | Environment | NY | $3,380,474Small | 92.17 |
| The BISON Children's Scholarship FundEIN 16-1477288 | Education | NY | $2,400,966Small | 96.77 |
| The Blue CardEIN 13-1623910 | Human Services | NY | $4,188,918Mid-sized | 94.13 |
| The Boomer Esiason FoundationEIN 11-3142753 | Health | NY | $6,494,763Mid-sized | 95.63 |
| The Bowery MissionEIN 13-1617086 | Human Services | NY | $16,832,525Large | 87.74 |
| The Boys' Club of New YorkEIN 13-5591750 | Human Services | NY | $12,451,748Mid-sized | 88.24 |