It all depends on what you want to get from the car and how much work you want to do.
If you want to drive it on the track I'd be looking for a nice NA engine that revs well, either a 20 valve or prefferably a built 16 valve.
If you want a nice simple conversion that makes the car feel tough around town 4AGZE is the go. They came with this engine making hte swap really easy. This also gives you a good building base to make a turbo setup in the future.
If you want to go to the trouble of doing a more extensive conversion then a 3S is the ticket. You could put in either the NA or turbo version of any generation. Since the amount of work to put any of the 3S's in would be about the same I went for the best one and put a Gen3 3SGTE in mine. Toby on these forums has a Gen3 NA engine in his AW11 and seems to enjoy it.
There really is no best engine conversion for any car. There are best value conversions, best power output conversions, best balanced etc but not simply best. A lot of people would say I'm mad for doing the work to get a 3SGTE into the car because I could have turboed a 4AGZE and got the same power. My priorities weren't based simply on maximum power though, so I made my decision based in my priorities and I recommend you do the same.