I would tend to agree with wopster. It's a pain to get to because of where the genius engineers put the filter but it can be done without removing any of the intake stuff, but prepare for a headache. that's your most probable culprit, followed by dirty injectors, which are easy to remove and clean, or remove and replace.
I would get yourself some feeler gauges and do a valve adjustment, just cause it's pretty easy to do and will only help the issue. Make sure you're running all factory stuff, plugs, wires, air filter, fuel filter, on Toyota's it's worth the money to run factory cause of durability and improved performance, unless you're running MSD ignition and such.
Just incase you don't have a shop manual, On the valve adjustment it's real easy. If you can get a set of go-no-go feeler gauges, makes it easier, as well as a valve adjustment wrench. If not, a 12mm wrench and screwdriver work fine. Get the engine warm. Pull the bracket with all your vacuum valves off and just fold it over onto the intake, then pull your valve cover off. Turn the crank to Top Dead Center for Cylinder 1. Cylinder 1 rockers should be loose. Then make the adjustment on intake valves on cylinder 1 and 2, and exhaust valves on cylinder 1 and 3. Loosen the nut on top of the rocker and either tighten or loosen the screw, then tighten the nut back down, then recheck clearance. Turn the crank over once (360 degrees) and adjust intake valves on cylinder 3 and 4, and exhaust valves on cylinders 2 and 4.
Double check all clearances after you've tightened the nuts back down and before you turn the crank over again. your clearances should be on your emissions tag, in case it's missing it's .20 mm (0.008 in) on intake, and .30mm (0.012 in) on exhaust.
Good tips. Probably want to at least inspect the cap, rotor, wires, plugs etc... I always like to do a standard tune-up when I get a new vehicle just cause you really don't have any history of when this was done, if ever!! Plus it is a pretty inexpensive way to eliminate stupid issues.
