Has Full Metal Alchemist Brotherhood always been the number 1 top anime on MyAnimeList?
On this reddit thread, you can see state of top anime list since 2007 until 2016. According to it, FMA: Brotherhood was outscored by Gintama at least for some period of time.

This history thread is not up to date, but at least it answers your question - yes, there was another top anime since FMA:B was released.