This is a very short, very lacking, list mostly trying to, or not, barring Naruto, because I honestly have too many favorites to list on here from that one, of my favorite ninja:
Sarutobi Sasuke (Sengoku BASARA) I have to say that, this guy, is probably my absolutely top favorite ninja of all time!
Fūma Kotarō (Sengoku BASARA)
Kinjō Shirasu (Donten ni Warau)
Hatake Kakashi (Naruto)
Senju Tobirama (Naruto)
Shiranui Genma (Naruto)
Hōzuki Suigetsu (Naruto)
... and I could go on and on and on. XD
So, now that you've been through all that... who's your favorite Shinobi or Kunoichi?