It can never easily be narrowed down to one character. In the Naruto series, Kishimoto often utilizes humor through the age-old methodology of the Double Act.
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In the double act/comedy duo, there is the serious "Straight Man"
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and then there is the "Funny Man."
Together the pair of characters complete the comedy act, rather just one or the other. A notable example outside of Naruto includes Abbot and Costello:
[video=youtube;WQXwt83hYkE]http://www.youtube.com/watch?v=WQXwt83hYkE[/video]
In other words, Kishimoto's humor is usually derived from interactions between a two or more characters rather than having one character alone be humorous in general.
For example, Tenten plays the 'straight man' role for Gai/Lee as the 'funny man' role.
Oddly enough, Gyūki plays the straight man role for Bee.
Sakura plays the straight man for Naruto.
Samui plays the straight man role for the pair, Karui and Omoi, who fulfill the funny man role together.
The list goes on and on...
It's never just one character that makes a comedy act in Naruto. It would be better to arrange a poll that consisted of best comedic character interactions.