How are you calculating your mileage?
Also, sounds like your tires are not stock size, are you correcting your calculations to take that into consideration? Bigger tires = fewer revolutions per mile, but the odometer doesn't know that, so the odo will read fewer miles than you actually drive.
When my off-road "summer" tires/wheels are on (BFG MTs in 255/75/17 on FJC steelies) I multiply my miles driven by 5.5% to take into account the error on the odometer. I came up with this number by comparing the odometer to a GPS tripmeter.
Also: What kind of driving do you do, do you let it warm up before you drive it and for how long, how long have you owned it, are you using 4wd, etc? There are a lot of variables when it comes to mileage.
Final note: If you are figuring mileage by the little gauge on the dash, forget it. We call that the "lie-o-meter" for a reason. It's worthless for calculating mileage.
The correct way to calculate mileage is this:
Fill the tank. Try to fill it the same way every time (for example, when I fill my tank I always "top off" by letting the pump shutoff twice. If that's the way you fill up, always do it that way.) If you really want an accurate measure, try to fill up at the same station or even the same pump, if possible.
After you fill the tank set one of the trip odometers to zero.
Then drive normally. Drive until your tank is down to 1/4 or lower.
Fill up again, fueling up the same way. Take note of the amount of fuel and miles driven. Miles driven / fuel consumed = MPG.
Now, if you are running bigger than stock tires, you'll need to figure out what your error calculation is before you can do the above. You'll need a decent GPS unit with a trip meter (almost all of them have this.)
Set the tripmeter on the 4runner to zero, and the tripmeter on the GPS to zero. Drive at least 100 miles (the more you drive, the more accurate your figure.) Make SURE the GPS is on at all times while the vehicle is moving or you'll get an incorrect reading.
After the 100+ miles, look at the number on the GPS and the number on the odometer. If your tires are bigger than stock, the GPS number will be higher than the truck's odometer number. Let's say you drive 100 miles exactly (as shown on the truck's odometer) but the GPS shows 96 miles. Divide the odometer number (100) by the GPS number (96) and you get 1.041 (IOW, a 4.1% error.)
Now, when you go to fill the tank, take the miles driven (let's say your odometer shows you went 355 miles) and multiply it by your "error" of 1.041. That means that while the odometer read 355 miles, you actually went 369.5 miles. Divide that by the amount of gas to fill the tank and that is your true MPG.