There is no best way to learn an instrument. Different things work for different people, and it really comes down to just putting a lot of time and love into your craft. I play drums, guitar, and I sing, scream and beatbox, and I'm pretty much self-taught with all of those. I did take drum lessons for awhile, but later stopped and now for most of my time playing the drums, I've learned things on my own.
Actually, calling myself 'self-taught' is kind of a lie in a way. I had many teachers, music I liked, other musicians, sounds I heard, everything. Getting lessons is good, but don't let that close you off to all the other great ways you can learn. Don't just take lessons from the same person for ages, learn from as many different sources as possible.
When it comes to learning anything, especially when it comes to the arts, sometimes it's best to take the formality and structure out of it.
And remember, academia and music theory tends to over complicate things. I play stuff on guitar that is a complicated mess when expressed in music theory, but just makes sense to my ear. Guitarists or musicians that can write and read the language, but can't speak it just get confused. A local guitar teacher around where I live always said "You wouldn't teach a baby to read and write before he can speak, would you? The same goes for music."