Your best bet would be the 1KD-FTV. Like the 1GD, you need to get the ones from Japan or those from Japan-made vehicles (Hilux Surf and Prado) because the ones from Thailand had the counter-rotating balance shaft removed. Also, oil consumption was a bit high in those vehicles from Thailand. But you'll have to be religious about maintenance, especially with the injectors (bit expensive). The 1KD is not as tolerant as the old diesel engines and one lapse could easily result in a cracked piston(s).

on the 1VD-FTV:
that's a pretty big and heavy engine. dunno how you're gonna fit that into the engine bay of the 4Runner.

Toyota had to modify the front frame of the LC70 to be able to make that engine fit. That resulted in a wider front track, but Toyota didn't change the rear so many aussies weren't happy about it. some have also transplanted that engine into the LC100 but dunno about the extent of modifications