I dont know if this applies in your case, but i had a similar problem, but i could feel the vibration if i kept my foot barely touching the gas pedal... turned out to be bad rear end gears and it happened when there was no positive or negative pressure on them (bad gear lash almost). Replaced the rear end gears and never had a problem since (70,000 miles when replaced... 110,000 currently)

1999 4-runner
TRD Supercharger, 5 speed, 2 inch pulley, Dual 2.5" exhaust, AEM Brute Force Intake, Supra Injectors