Applejack is portrayed as strong, independent, and very dedicated. She isn't the best at much, but she is extremely talented. Compare:
Rarity: Rarity runs a one-mare business. Applejack runs a family business with at least two other workers (Big Macintosh and Granny Smith.)
Pinkie Pie: Pinkie Pie is known for throwing spur-of-the-moment parties. Applejack's parties have live music, pumpkin cannons, spider targets, and a much wider range of foods. (As long as they have apples.)
Rainbow Dash: Rainbow Dash is known for her speed in the air. Without her wings, she's almost exactly the same speed as Applejack.
Fluttershy: Fluttershy can comfort skittish animals. When she's not tired, Applejack and Winona can stop a stampede. (When she is tired, she starts one. Of bunnies. Nobody's perfect.)
Twilight: Twilight has two talents: Magic and organizing. Applejack doesn't have the magic talents, but winter wrap-up showed that she's almost as good at organizing. Her team got rid of all the snow!
None of the other ponies are as broadly talented.
Therefore, Applejack is best pony.