| Stony Brook Internists, University Faculty Practice Corporat | Health Care and Social Assistance | $4,903,019 | $4,956,751 | 271 | N/A |  Research |
| Faculty Student Association at Stony Brook University | Administrative and Support and Waste Management | $3,627,500 | $3,666,359 | 386 | N/A | Research |
| Stony Brook Surgical Associates, University Faculty Practice | Educational Services | $1,932,882 | $1,950,357 | 104 | N/A | Research |
| Stony Brook Anaesthesiology, University Faculty Practice Cor | Educational Services | $1,622,927 | $1,634,488 | 75 | N/A | Research |
| Stony Brook Foundation, Inc. | Other Services (except Public Administration) | $1,424,045 | $1,440,947 | 307 | N/A | Research |
| Stony Brook Emergency Physicians, University Faculty Practic | Educational Services | $1,360,727 | $1,375,676 | 75 | N/A | Research |
| The Stony Brook School | Educational Services | $1,308,100 | $1,317,584 | 130 | N/A | Research |
| Stony Brook Psychiatric Associates University Faculty Practi | Educational Services | $1,288,297 | $1,302,451 | 81 | N/A | Research |
| Stony Brook Radiology University Faculty Practice Corporatio | Health Care and Social Assistance | $1,200,900 | $1,209,224 | 59 | N/A | Research |
| University Associates in Obstetrics & Gynecology Univers | Other Services (except Public Administration) | $1,192,010 | $1,200,305 | 66 | N/A | Research |
| Applied Dna Sciences INC | Professional, Scientific, and Technical Services | $846,789 | $853,633 | 48 | $10.0M | Research |
| Ring Savvy, INC | Administrative and Support and Waste Management | $751,547 | $758,791 | 116 | $21.9M | Research |
| Stony Brook Orthopaedic Associates University Faculty Practi | Educational Services | $683,119 | $687,891 | 33 | N/A | Research |
| Neurology Associates of Stony Brook, Ufpc | Health Care and Social Assistance | $641,415 | $647,179 | 36 | N/A | Research |
| Ljtm Group, Inc. | Accommodation and Food Services | $617,700 | $624,368 | 26 | <$5M | Research |
| Long Island Adolescent & Family Services | Health Care and Social Assistance | $594,017 | $598,297 | 78 | N/A | Research |
| New York Spine & Brain Surgery University Faculty Practi | Health Care and Social Assistance | $563,925 | $567,849 | 29 | N/A | Research |
| Stony Brook Pathologists, University Faculty Practice Corpor | Health Care and Social Assistance | $543,997 | $549,988 | 26 | N/A | Research |
| Stony Brook Child Care Services INC | Health Care and Social Assistance | $521,485 | $525,585 | 60 | $9.7M | Research |
| Biocogent, LLC | Manufacturing | $485,167 | $489,341 | 32 | $31.7M | Research |
| Stony Brook Family and Preventive Medicine University Facult | Educational Services | $457,175 | $462,210 | 26 | N/A | Research |
| Thermolift, INC | Professional, Scientific, and Technical Services | $453,610 | $459,191 | 25 | $5.2M | Research |
| Mcmullen & Young Ltd | Accommodation and Food Services | $438,200 | $441,622 | 35 | $6.2M | Research |
| Stony Brook Child Care Services INC | Health Care and Social Assistance | $378,135 | $379,938 | 33 | $5.3M | Research |
| The Gottesman Organization , Inc. DBA Al Tus Metal & Ma | Construction | $372,602 | $376,771 | 25 | $8.5M | Research |