Here is an MPG comparison taken from Toyota.com of the following trucks-
4.0 V6 PreRunner Access Cab AT- 17/21
2.7 I4 4x4 Access Cab AT- 18/21
2.7 I4 4x4 Access Cab MT- 18/20
As you can see, basically no difference.
I remember seeing the 0-60 times on all the Toyota models in some kind of PDF file fact sheet on this site. Wish I could find it again. Anyway, the 4.0 blows the 2.7 with either tranny out of the water, and the 2.7 manual was like 2 full seconds or more, faster than the 2.7 auto if I remember right. I was thinking about trading my 5-speed reg cab 4x4 for the auto version, but once I saw that, there was no way I was going to do it. The 5 speed barely has enough power IMO.
Do you need 4x4? If so, get a 2.7 if its all you can afford (not hating, I have a reg cab 4x4 because it's all I could afford). I would REALLY encourage you to get the manual if you do go with the 2.7 for the power reasons though.
Do you not need 4x4? If so, and especially if you need to tow, get the V6. I've honestly been looking to trade my 4x4 regular cab for a V6 access cab PreRunner. The 09s and newer PreRunners can handle snow and light offroading just fine in my opinion.
Want more honest answers, and not just someone supporting THEIR truck, PM me.