Bleach: Action Girl Yoruichi. She used to have short hair, but a hundred years spent mostly as a cat allowed her hair to grow out. Now she spends most of the time with it tied back in a ponytail while she kicks butt with the best of the men. Since her extremely high aristocratic rank wasn't quite high enough to be a Rebellious Princess, she also doubles as a Spirited Young Lady, too.
Presea from Magic Knight Rayearth. Also, tomboys Tarta and Hikaru have their hair in a braid. Contrast to the girlier girls Emeraude, Alcyone, Tatra, and Umi, who wear their hair down. Caldina, Fuu, and Aska are harder to classify, since they have both tomboy and girly girl traits, but all wear different hairstyles.
Kyoko Sakura of Puella Magi Madoka Magica. While her magical girl outfit isn't really tomboyish, she's the only character seen in causal clothes other than a school uniform (she wears a blue hoodie and shorts in most scenes).
Ukyou from Ranma ½ wears her waist length hair in a ponytail and still comes off as Bifauxnen.
Ranma wore "her" long hair this way while training in China.
Subverted in the Pretty Cure franchise. Every team has atleast one character with a ponytail who is mostly a white or blue Cures. And those said Cures are actually the most feminine members, though that doesn't stop being an (competent) Action Girl. The only blue Cures who don't have a ponytail in their Cure forms are Cure Marine (Erika) and Cure Beauty (Reika), but they wear sometimes ponytails in their civilian identities. Notably, Reika wears a ponytail whenever she practices kyudo. The pink Cure Blossom and the yellow Cure Peace have also a ponytail, but both are Shrinking Violets, while the pink Cure Heart is atleast described as prince in her civilian identity, twice, both by a female and a male. The only ones who play this tropes straight are Cure Sword and especially Cure March who has also one in her civilian identity.
In The Movie, Reika cosplays Momotaro and wears a ponytail.
Bait and Switch (STO): Captain Kanril Eleya wears her hair in a slightly messy ponytail, and notes in her narration that she could have never gotten away with wearing her hair that long when she was an enlisted woman. The ponytail keeps the hair out of her face, but it's not like there's much she can get it caught in on a starship's bridge.
Cady in Mean Girls before she joined the Plastics. The Plastics actually tell her that they have a rule about only wearing hair in a ponytail once a week.
Nanase of El Goonish Shive tends to wear her hair this way when it it is the appropriate length for it.
Widget of the Whateley Universe, who is a tomboy and inventor who usually wears a ponytail pulled through a bicycle cap. And a Whateley labcoat. Despite that, she has a bad crush on Thunderbird and wishes Chaka hadn't snatched up Thunderbird when he was (apparently) available.