We have a Yakima roof rack, a nice Thule roof rack, a Kuat NV hitch rack, and a 1Up USA hitch rack. We've had a few others in the past - we've just about tried them all...
Here are my observations:
I tried the front bike wheel over truck tailgate thing for a while, and I just didn't like it. I always felt like I was on the verge of damaging the bike (or the truck). With a 4runner, getting part of the bike through the rear window seems like a hassle. And what if it's raining or snowing (we ride bikes in the snow here

)
On a 4runner, I definitely prefer the hitch racks - they are plenty stable, the bikes are more protected (IMHO - I'm not paranoid about being rear-ended, and If I am, the other guy's insurance will probably be on the hook). Also, getting bikes, particularly beefy mountain bikes on the roof of a 4runner is not trivial...my wife can't do it.
Of the hitch racks I prefer the 1Up - the build quality is pretty crazy, they are stupid simple, every part is replaceable, and I love the staggered tray heights. It can really help with bar/saddle interference. And with the factory extender gizmos, they are truly fatbike friendly!
Downsides of the 1Up: Expensive, and no integrated lock for the bikes. But a basic cable lock does the trick.
Also, the idea that there is no pin through the receiver hitch on the 1up freaked me out for a while. I actually thought about trying to drill a hole for one. But I think there's good reason you never hear horror stories of one of these falling off the back of a vehicle - it does not budge, thanks to the proprietary securing mechanism.
If you have to go with a roof rack (we need them because we often tow a camper), Thule over our Yakima here. But that's a closer call...I just absolutely hate the yakima rear wheel straps.