At low ISO, yeah, the 100D does ok, but if you need to push it, than the D3300's the better way to go. As much as I do like the 100D, higher ISO is cleaner on the D3300, simply put.
I'm not going to knock the D90 either. It was never a slouch. But again...it's outdated.
I was thinking about d3300 but my wife likes canon ... the d90 was a bit of an interest cause it cost the same plus has some better features and also built in motor