Someone else on here has the Alpine IVA-W200 which is a 2-DIN unit in theirs. If his fits, the Clarion should too, but I have no basis or experience with it. Like said, find out the face measurements of the stereo you are looking at, and measure the opening in the dash.
And if Metra makes an install kit for it to mate to your 4Runner, then you KNOW it will fit.
Edit: I just went out and measured my stereo in my 4Runner, it measures 4.0" by 7.8"
And by checking on Metra's website, it shows the stock unit as a Double DIN unit.
Install kit number 95-8202 should adapt a double din aftermarket stereo to fit in your dash, and wire pigtail number 70-1761 will allow you to make an adapter that will plug into the aftermarket stereo, and the Metra pigtail will plug right into the factory harness, so when it's time to sell the vehicle, all you do is pull the stereo, unplug it, slap in the factory one, and the dealer/buyer will never know you ever had anything else in it. Plus you dont butcher the wire harness of the car, leaving it completely intact. This is how I install ALL my stereos, and it make changeovers/upgrades/repairs a breeze. I can usually pull my Alpine out, and put the stocker back in, within ten minutes.
Here is the
Metra site's info.