The 39 Miku day concert was held in Zepp Tokyo, which according to Wikipedia, has a capacity of around 2000 seats. It's "merely" a concert hall, not a stadium, but I think that's pretty good for a voice synthesizer.
The debut album featuring Hatsune Miku by supercell managed to top out at #4 on Oricon's weekly rankings for music sales when it was released. Also, if you take a look at Joysound, a major karaoke vendor in Japan that added Vocaloid songs to their catalog, Vocaloid songs occupy 9 out of the top 15 spots in the current weekly rankings across *their entire catalog*, not just the anime-related stuff. It missed out of the top 3, with those going to two AKB48 songs and the Eva opening song. So yes, not more popular than AKB48, but not totally unknown either.