Nix from Cruel Beauty by Rosamund Hodge: This girl is fierce and broken and wonderful.
Otter and Kestrel from Sorrow's Knot by Erin Bow: These two have complementary but equally important skills and their friendship and the way they work together is beautiful.
Elisa from The Girl of Fire and Thorns trilogy by Rae Carson: Elisa is a heroine who grows into her power and awesomeness. It's a delightful story to experience.
Tori from Quicksilver by R.J. Anderson: She's an engineer, a genius, and so tough and dedicated to the paths she chooses for herself it's mind-boggling.
Tiffany Aching from The Wee Free Men (and sequels) by Terry Pratchett: Tiffany Aching is the reason the phrase "made of awesome" was born.
Other Heroine Lists: MG Speculative Fiction