Shikamaru. Why is this even a question when Kishimoto tells you he is the smartest!
its simple Itachi's the smartest!
Shikamaru's over 200 IQ says otherwise. Shikamaru is on a different level than Itachi. 200 plans in a second. Can think 10 moves ahead of you. Always making the right choice. He is a freaking computer. The only thing that keeps him from being a god-like character in Naruto is that he is lazy as hell and has no ambition. Characters like Itachi, Madara, Minato care. Shikamaru doesn't. The guy never trains a second! Other geniuses like Neji and Sasuke also work hard. Shikamaru never has to and yet he still is thought of as a Hokage candidate. All based on how smart he is.
Shikamaru is the easily the smartest Naruto character. No one has his potential with intelligence. Not even his father who should be considered the smartest character right now. He is the one character who Kishi always stresses his intelligence above others. Even Kakashi passed the torch to him during the Zombie Twin Arc. Very few people in the history of the world were thought to have an over 200 IQ. So Kishi used a real world stat to show that no one can pass Shikamaru. But his laziness will make sure he never reaches his potential.
For a comparison look at the current databook stats with intelligence and cunning. Neji is a 3. Sasuke is a 3.5. Shikamaru had a 5 at age 12! He could have been a chuuin at age 5 if he wasn't so damn lazy. He makes Neji and Sasuke, two intelligent characters, look like idiots.