From a writer's perspective, it's easy to empathize with the poor portrayal of Naruto and Sasuke's friendship. Sometimes, when you write things, you have this very clear picture in your head of what you want to create, and in the process of translating that picture into actual consumable material for others the idea doesn't come across as well as it did during its conception. Kishimoto has admitted that he didn't frame their friendship as well as he wanted to, but they were definitely always meant to have a close bond in his eyes.
I guess, from a reader's standpoint, we can only assume that most of their bonds were formed in their childhood, in the classroom and in the missions that they undertook in between Land of Waves and the Chunin Exams. It's not like it wasn't there in early Naruto either, though - the training scene in the woods where they're climbing trees is still one of my favorite in the entire series, especially when they come back to Tazuna's and eat up a storm from all the energy they expended.