Hattori Hanzo Masasige is the best ninja imho.
Sarutobi Sasuke is a fictional character and historians think that his character is based on Simotsuge Kidzaru also known as Uedzuki Sasuke from Iga.
The following people were confirmed to be historical ninjas. Sorry, if my spelling is not very accurate. Also ninjas that were born after the death of Tokugawa Ieyasu are not mentioned here but I can assure you that Masaaki Hatsumi is not a ninja, though he is a great martial artist
Iga:
1. Hattori Hanzo Yasunaga
2. Hattori Hanzo Masasige - son of Hattori Hanzo Yasunaga and the famous bodyguard of Tokugawa Ieyasu
3. Fudzibayasi Nagato-no Kami
4. Momoti Tamba Yasumitsu (Momoti Sandayu) - could be another name for Fudzubayasi Nagato-no Kami
5. Nomura Oi Magodayu
6. Sindo Kotaro
7. Tateoka (Igasaki) Mitidzun
8. Simotsuge Kidzaru (Uedzuki Sasuke)
9. Simotsuge Kodzaro - possibly the son of Simotsuge Kidzaru
10. Ueno Hidari (Takava Sahei)
11. Yamada Hatiemon (Yaemon)
12. Kambe Konan
13. Otova Kido - could be another name for Igasaki Mitidzun, famous for trying to kill Nobunaga
14. Takayama Tarosiro
15. Takayama Tarodzaemon
16. Isikava Goemon - famous for trying to kill both Toyotomi Hideyoshi and Oda Nobunaga
17. Momoda Tobei
18. Yokoyama Dzinsuke
19. Fukukita Syogan
20. Mori Sirodzaemon
21. Matii Kiyobei
22. Yamado Kansiro
Koga:
1. Yamanara Dzuro
2. Saga Etidzen-no Kami
3. Miyadzimi Kamimoribenosuke
4. Kuradzi Ukonnosuke
5. Hirano Tonomorinosuke
6. Katsuragi Tango-no Kami
7. Sugitani Yototsugi
8. Kiyama Sikanosuke
9. Motidzuki Idzumo-no Kami
10. Vada Iga-no Kami
11. Hari Idzumo-no Kami
12. Oki Ukon Taro
13. Akutagava Sakyomaru
14. Uda Tonai
15. Torii Heinai
16. Sugiyama Hatiro
17. Hattori Totaro
18. Okavahara Gennai
19. Okubo Gennai
20. Sadzi Kavati-no Kami
21. Takamine Kurando
22. Ohara Gendzaburo
23. Ban Sakyonosuke
24. Makimura Umanosuke
25. Uenosyu Yosimasa
26. Taki Kantaro
27. Noda Goro
28. Ivane Nagato-no Kami
29. Kogava Bunnai
30. Ugai Genhatiro
31. Kogava Magodzuro
32. Yamakami Tositiro
33. Hata Kansuke
34. Hayami Sihonosuke
35. Kamiyama Sinhatiro
36. Ivamuro Daigakunosuke
37. Nakayama Minobedzyo
38. Takayama Gendaidzaemon
39. Ikeda Syoemon
40. Nagano Kyobudzyo
41. Utiki Iga-no Kami
42. Ono Miyauti Syoho
43. Sindzyo Etigo-no Kami
44. Aoki Tikugo-no Kami
45. Koidzumi Gaiki
46. Natsumi Daigaku
47. Tarao Sirobei
48. Niva Mikumo Sindzobito
49. Minobe Genkiti
50. Akimoto Kodzukenosuke Masahide
51. Dzimbo Heinai
52. Takamatsu Ise-no Kami
53. Aeba Kavati-no Kami
54. Takano Bingo-no Kami
55. Nino Kuranosuke
56. Tatsumi Niro
57. Honda Tikudzen-no Kami
58. Uenisi Bego
59. Kidono Yamato-no Kami
60. Endo Musyanosuke
61. Sekiguti Gondzyuro
Negoro:
1. Suginobo Myosan
2. Ivamurobo - first name not known
3. Sensikibo - first name not known
4. Akaibo - first name not known
5. Negoro Denko - organized his own school within Negoro-ryu
Ninjas of Tokugawa:
1. Hattori Gensuke
2. Hattori Dendziro
3. Hattori Den'emon
4. Hattori Magobei
5. Hattori Utikura
6. Hattori Sinkuro
7. Hattori Kanroku
8. Tsuge Sannodzyo
9. Tsuge Itinosuke
10. Tsuge Kanhatiro
11. Yamaoka Sobei
12. Yamaoka Sukedayu
13. Tomita Yahei
14. Fukumori Sadanari
15. Yamanaka Tobei
16. Kikuti Toyofusi
17. Sibata Suho
18. Yoneti Hansuke
19. Yamaguti Kansuke
Other:
1. Idaten - real name not known, from Omi, worked for Hideyoshi
2. Fuma Kotaro - worked for Hojo
3. Tomito Godzaemon - worked for Takeda Shingen
4. Motidzuki Tiyomo - famous kunoichi of Shingen
5. Usami Suraga-no Kami Sandayuki - worked for Uesugi Kenshin, there are still some doubts about him being a ninja.
6. Kadzi Omi-no Kami Kagahide - worked for Kenshin.
7. Sada Hikosiro - the most talanted of Sada brothers, worked for Mori
8. Sada Dzingoro (Goro) - Hikosiro's and Konedzumi's brother, worked for Mori
9. Sada Konedzumi - brother to Hikosiro and Goro, worked for Mori
10. Saiga Magoichi Sigetomo - founder of Saiga-ryu, studied ninjutsu in Negoro-ryu
11. Fudzibayasi Yasutake - theoretically belongs to Iga school, author of an important book on Ninjutsu
12. Fudzibayasi Masatake - Yasutake's brother, an author of another masterpiece on Ninjutsu, founder of his own school and a follower of Iga-ryu
13. Hatisuka Tendzo - worked for Nobunaga, tried to kill Takeda Shingen
14. Kato Dandzo - was a real ninja but his deeds are extremely exaggerated now.
15. Sugitani Dzendzyubo - believed to be a ninja from Koga, tried to kill Nobunaga
16. Satoru Doken - Koga ninja, worked for Takeda, tried to kill Nobunaga but was killed by Hattori Hanzo
17. Manabe Rokuro - another unlucky hunter for Nobunaga's head, possibly from Iga
Legends and myths:
1. Kempati Dzinnai - Uesugi Kenshin was not killed by this ninja in a toilet. This is the most popular myth in the history of ninjutsu. Dzinnai never existed.
2. Sarutobi Sasuke - mentioned in the beginning of the post.
3. Kato Dandzo - see "other, 14."
There were lots of other ninjas but they were not that important. Sorry for such a huge post, but may be some people will find it interesting and helpful
There's no trick to it. I'm not using an orbment, it's not magic...and I'm not using an artifact, either. I just will fire to appear, and it does.
McBurn