BronyNet has ~22,000 members, Ponysquare ~10,000.
According to this http://siteanalytics.compete.com/equestriadaily.com/?metric=uv, Equestria daily has ~86,000 unique visitors per month.
We could think about many pony communities coexisting, but my guess is there is overlapping. For this reason my guess the size of the brony community in 2012 is ~50,000. Where brony is someone who participates in a website related to FIM.
But if brony is someone who has watched FIM and likes it, the number could be higher. I think for everybrony there are 10 persons who watches and likes the show in the same demographic. So ~500,000.