Personally, I think Dangerous is his best album.
As far as Thriller, it absolutely could be number one and any arguement as to why it SHOULD be is legit. It's the biggest, most well-known and successful album ever.
But, because I'm also a Stevie fan and have a lot of knowledge on "Songs In The Key Of Life", I've heard in interviews where MJ said how he was mesmerized when he got to sit in the background and watch Stevie create the masterpiece. The album is 2-Discs and has everything from jazz, funk, R&B, pop, soul... some of the songs to me are as haunting as people describe "Billie Jean". Listen to "Another Star": on the top, it's a latin-tinged beast of a dance/party track. Underneath, it's a song essentially saying that his former love might be able to move on, but he will not. ("For you, there might be a brighter star, but through my eyes, the light of you is all I see."). It's really awesome how the tone and lyrics are total opposites, yet the song still works beautifully.
"Love's In Need Of Love Today" is one of the first popular peace anthems: it's a precursor to "We Are The World" and "Man In The Mirror". ("Hate's goin' round, breaking many hearts. Stop it please, before it's gone too far.")
We all know how awesome "I Wish", "Sir Duke" and "Isn't She Lovely" are.
"As" is a beast of a song... an epic piece of song writing.
"Joy Inside My Tears" sounds like someone laughing and crying simultaneously, it's got a very sublime tone.
It's a massive album full of Stevie doing almost all of the writing and much of the instrument-playing himself, with top collaboration with engineers and instrumentalists. I can see why this album is number one.