| Rank | City | 2000 Population |
|---|---|---|
| 1 | Baxter Estates | 1,007 |
| 2 | Otisville | 991 |
| 3 | Poquott | 977 |
| 4 | Millerton | 927 |
| 5 | Richmondville | 786 |
| 6 | Tuxedo Park | 731 |
| 7 | Hammondsport | 730 |
| 8 | Elba | 694 |
| 9 | Schaghticoke | 675 |
| 10 | Interlaken | 674 |
| 11 | Oneida Castle | 626 |
| 12 | Chaumont | 608 |
| 13 | Cato | 600 |
| 14 | Riverside | 593 |
| 15 | Middletown | 25,371 |
| 16 | Cherry Valley | 590 |
| 17 | Bridgewater | 583 |
| 18 | Van Etten | 581 |
| 19 | Barker | 576 |
| 20 | Nichols | 572 |
| 21 | East Nassau | 570 |
| 22 | Wampsville | 560 |
| 23 | Rockville Centre | 24,573 |
| 24 | Cherry Creek | 550 |
| 25 | Middleville | 549 |
| 26 | Remsen | 530 |
| 27 | Ossining | 24,098 |
| 28 | Milford | 516 |
| 29 | Wyoming | 512 |
| 30 | Hewlett Neck | 506 |
| 31 | Hewlett Bay Park | 485 |
| 32 | Ellicottville | 480 |
| 33 | Poland | 461 |
| 34 | Leicester | 461 |
| 35 | Morristown | 455 |
| 36 | Centre Island | 444 |
| 37 | Clayville | 444 |
| 38 | Limestone | 410 |
| 39 | Pike | 381 |
| 40 | Sagaponack | 355 |
| 41 | Meridian | 350 |
| 42 | Rensselaer Falls | 336 |
| 43 | Prospect | 329 |
| 44 | Madison | 312 |
| 45 | Dresden | 306 |
| 46 | Constableville | 305 |
| 47 | Gainesville | 303 |
| 48 | Ellisburg | 268 |
| 49 | Turin | 263 |
| 50 | Ames | 173 |
| 51 | Ocean Beach | 138 |
| 52 | Depew | 16,571 |
| 53 | Tonawanda | 16,099 |
| 54 | Floral Park | 15,969 |
| 55 | Cohoes | 15,593 |
| 56 | Johnson City | 15,476 |
| 57 | Rye | 14,970 |
| 58 | Glens Falls | 14,329 |
| 59 | Endicott | 12,989 |
| 60 | Massena | 11,179 |
| 61 | East Rockaway | 10,368 |
| 62 | Hamburg | 10,087 |
| 63 | Mount Kisco | 10,011 |
| 64 | Newark | 9,680 |
| 65 | New Hyde Park | 9,534 |
| 66 | Potsdam | 9,518 |
| 67 | Amityville | 9,450 |
| 68 | Hornell | 9,137 |
| 69 | Woodbury | 8,865 |
| 70 | Malverne | 8,940 |
| 71 | Johnstown | 8,615 |
| 72 | Ilion | 8,604 |
| 73 | Brockport | 8,096 |
| 74 | Rensselaer | 7,879 |
| 75 | Port Jefferson | 7,855 |
| 76 | Croton-on-Hudson | 7,625 |
| 77 | Northport | 7,613 |
| 78 | Norwich | 7,341 |
| 79 | East Aurora | 6,658 |
| 80 | Irvington | 6,639 |
| 81 | Bronxville | 6,545 |
| 82 | Monticello | 6,525 |
| 83 | Larchmont | 6,492 |
| 84 | Medina | 6,408 |
| 85 | Salamanca | 6,084 |
| 86 | Malone | 6,062 |
| 87 | Albion | 5,954 |
| 88 | Hilton | 5,885 |
| 89 | Fairport | 5,734 |
| 90 | Goshen | 5,711 |
| 91 | Pelham Manor | 5,469 |
| 92 | Le Roy | 4,455 |
| 93 | Catskill | 4,388 |
| 94 | New Square | 4,352 |
| 95 | Springville | 4,285 |
| 96 | Fayetteville | 4,184 |
| 97 | Dannemora | 4,083 |
| 98 | Liberty | 4,013 |
| 99 | Ellenville | 4,004 |
| 100 | Portville | 1,022 |
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