At first, I thought Equestria Girls was the best movie. But I think that was mostly because it was the first one I saw and had a lot of stupidly funny moments.
After watching them all through multiple times though, I'm gonna have to say Rainbow Rocks is best movie. The music is fantastic, the Dazzlings were so amusing to watch (and dem voices~) and best of all, Trixie played a part (she needs more love). Plus, the ending I liked a lot. Felt more like an equal battle with the Dazzlings vs Rainbooms, as opposed to the ending of the other two 'villains' which seemed rather short-lived.
So I'm gonna say 1. Rainbow Rocks, 2. Friendship Games, then 3. Equestria Girls.