Long post so here is the summary, go with the Thule Sonic box in a minimum size of XL and Thule aerobars with crossroad feet if you need crossbars.
In the winter I work at a shop that sells both Thule and Yakima. If your 4runner already has factory crossbars you can go ahead and get a cargo box to mount to them. I personally use a Thule Sonic XL. It is a good compromise between cost and performance. The difference between a cheap box and a higher end box is mostly ease of attaching it, rigidity, wind noise and fuel economy. Having the box is great, I have more room for gear on the way to the lake and on my way home I don't have to put any wet gear in my car. I have also seen people use the clamping style snow ski carriers. These will work but you won't have any protection for your gear, no where to put your wet vest and the wind noise will be louder.
If you don't have crossbars of your car or want to go with a really large box like a xxl or xxxl Sonic you will want/need to get some aftermarket crossbars. With the 4runner you probably have two rails on the roof running from front to back. You can attach the crossbars to those rails. One bonus to having the rails is that next time you get a car you can swap your rack to the new car so long as it also has rails and is a similar width. For a vehicle with rails I suggest going with Thule.(unbiased opinion, I have both Thule and Yakima Whispbars for my vehicles) Their rail grabbing system is the best and has the least amount of moving plastic parts. The only reason I would go with Yakima Whispbars over the Thule bars for the 4runner is if you want to be able to put accessories on and off really fast or it you will be changing vehicles a lot.
If you are going to leave your rack on for the whole summer I suggest going with aero bars instead of square bars. The wind noise and dip in fuel economy is much better with aero bars especially if you have a sunroof or like to drive with the windows down.
Summary go with the Thule Sonic in a minimum size of XL and Thule aerobars with crossroad feet if you need crossbars.