I found this map of NYC Charter school on this website. Seems to me the Bronx and Brooklyn top out the list of charter schools in NYC.

SCHOOLS BY BOROUGH

Bronx

2. Bronx Charter for Better Learning
3. The Bronx CS for Children
4. Bronx Global Learning Institute for Girls
8. Family Life Academy Charter School
10. Grand Concourse Academy Charter
16. South Bronx Charter School for International Cultures and the Arts
17. South Bronx Classical Charter School
18. The Bronx Charter for the Arts
21. Bronx Academy of Promise Charter School
22. Bronx Charter School for Excellence
23. Bronx Community Charter
25. Icahn Charter School 1
26. Icahn Charter School 2
27. Icahn Charter School 3
38. Harriet Tubman Charter School
52. Bronx Lighthouse Charter
58. Hyde Leadership Charter
59. KIPP Academy Charter School
68. Bronx Preparatory Charter School
79. Green Dot New York Charter School
80. International Leadership Charter School
82. New York City Charter HS for Architecture, Engineering, & Construction Industries

Brooklyn

5. Brooklyn Charter School
6. Community Partnership Charter School
7. Community Roots Charter School
12. La Cima Elementary Charter School
20. Beginning with Children Charter
24. Brooklyn Excelsior Charter
29. East New York Prep Charter
30. Excellence Charter School of Bedford Stuyvesant
31. Explore Charter School
39. Hellenic Classical Charter School
40. Leadership Prep Charter School
43. PAVE Academy Charter School
45. Achievement First Brownsville Charter School
46. Achievement First Bushwick CS (Elementary)
47. Achievement First Bushwick CS (Middle)
48. Achievement First Crown Heights CS (Elem.)
49. Achievement First Crown Heights CS (Middle)
50. Achievement First East New York Charter School
51. Achievement First Endeavor Charter School
53. Brooklyn Ascend Charter
60. KIPP AMP Charter School
67. United Federation of Teachers CS (Elementary)
69. Bedford Stuyvesant Collegiate Charter
71. Kings Collegiate Charter
74. Williamsburg Collegiate Charter School
77. United Federation of Teachers CS (Middle)
83. Williamsburg Charter HS

Manhattan

1. Amber Charter School
9. Girls Preparatory Charter School
11. Harlem Day Charter School
13. Manhattan Charter School
15. Sisulu-Walker Charter School of Harlem
19. Harbor Science & Arts Charter School
28. DREAM Charter School
32. Future Leaders Institute Charter
33. Harlem Link Charter School
34. Harlem Success Academy
35. Harlem Success Academy 2
36. Harlem Success Academy 3
37. Harlem Success Academy 4
41. Mott Haven Academy Charter
55. Harlem Children’s Zone Promise Academy I Charter Upper Elementary, Middle
56. Harlem Children’s Zone Promise Acad I High
57. Harlem Children’s Zone Promise Academy II Charter Elementary School
59. KIPP Academy Charter School
61. KIPP Infinity Charter School
62. KIPP STAR College Prep Charter School
65. Ross Global Academy Charter
66. St. HOPE Leadership Academy
70. Harlem Village Academy
72. Leadership Village Academy
73. New Heights Academy Charter School
75. Democracy Prep Charter School
78. New York Center for Autism Charter School
81. John V. Lindsay Wildcat Academy Charter School

Queens

14. Peninsula Preparatory Academy Charter
42. Our World Neighborhood Charter School
44. VOICE Charter School
63. Merrick Academy Queens Public Charter School
64. The Renaissance Charter School