At this point, ToneX just sounds better.
Amplitube was more of a cross between captures and algorithms, to my understanding.
ToneX is more like impulse response captures.
ToneX does work inside Amplitube, where you can add all the Amplitube things like, other amps (for multiple amp setups), pedals on a pedalboard and post-cabinet rack-style effects. Both allow for mixing and matching cabinets.
There is an update for ToneX that will be adding more effects, but Amplitube still allows for more complicated setups overall.