If the RAV4's towing capacity is 3500 with the tow package it has, then that's what the engineers have spec'd for it. The only advantage of the Tacoma I could see is that it is heavier than the RAV4 (I would think, but maybe not with the 4 cyl engine), and the wheel base is longer, so the truck may be a little smoother when towing and handle a little better. I don't know these vehicles personally, so perhaps someone else with experience on these two can shed more light.
I would prefer the 6 cyl of the RAV4, but would also prefer the longer wheelbase of the Tacoma for a more stable towing experience. Sorry, not much help ;-)