I'd say that FMA:Brotherhood is arguably the best shounen ever; though I prefer Steins;Gate in story personally.
Reasons being: Time-travel concept has been so often awfully shown in shows/movies with lots of flaws; that seeing an anime on it without any plotholes, deserve applaud. Steins;Gate hits all the right spots besides in my opinion in all sections. Save for a slow-paced start, it's arguably flawless in its story. So, I'll closely edge it above!
I'm tempted to mention instant classics like Death Note & Code Geass and timeless classics like Cowboy Bepop that are close-contenders.
One Piece and Naruto are very good in delivering a story on a lengthy time period in a vast shounen world. In that way, it's very good; especially One Piece for better creativity. Kudos to recent animes like Psycho-Pass & Shingeki no Kyojin who also got great story.