Altezza makes a transmission? I thought they only made crappy taillights, headlights & intakes, that leak like a sieve, for the Fast & Furious crowd of douche bags.
Pretty much all your options are laid out here. W-series bellhousing from an SA6x Celica is probably your best bet, for ease of acquisition. The 6-speed from an Altezza would be nice, but I know very little about the durability or technical specifications of this transmission, so if someone with any more experience is telling you that it doesn't like torque, you should probably consider that.
The W58, as we all know, likes to strip out third gear for no reason when power is applied to it. It all depends how much power your 3s-gte is going to put out.
I didn't know that little bit of trivia about the Y-series motor having the same bellhousing bolt pattern as the S-series.