Ultimately id opt for the water to air intercoolers, just remember any top mount intercooler is going to have to be big to gain a difference. My mechanic is a Nismo performance centre mechanic and says for me to go for a front mount, might be a bit hard as i dont have much room, but to do it anyway, to have a top mount to do the same job as a front one it would have to be 3 times the size of the front mount cooler after you factor in differences with heat, less air flow etc etc.
My mate with his 2.8d patrol has got a top mount cooler with factory fan underneath it, on his patrol forums guys reckon at 80km/h the scoop gets stuff all air, cos of the way the bonnet is shaped with the scoop, and has been advised to fit a bigger scoop.