I work for a Ford dealer, and our pre-owned lot sells plenty of other brands. As long as the dealer has a good reputation and the vehicle has a standard warranty, then you're probably fine. You won't get a certified pre-owned vehicle this way, but you'll get a cheaper price. CPO Ford vehicles, and I assume everyone else's are similar, are thoroughly inspected and reconditioned and bundled with an extended warranty of up to 100,000 miles. They're a good deal, but not the lowest-price one.
The buyers at my lot only stock good, quality vehicles. If it comes in through trade, its something in excellent shape and low to average miles. If its from auction (most are), the same conditions apply. Most dealers do it that way.
As for your choice in vehicle, why are you interested in the 4Runner? I'd recommend the Expedition or Explorer from Ford.
I used to be a Ford hater. I learned to drive on a Ford Tempo... 'nuff said. But Ford has come a LONG way in recent years. They have high-quality vehicles and the overall best fuel-economy of any major manufacturer. Look at what Consumer Reports is saying. The 2009 Fusion versus the 2009 Toyota Camry... the Fusion kicked the Camry's butt all over the place. And if you're going for a truck, and essentially the 4Runner and Expedition are trucks with more seating room, Ford is THE truck leader.
Anyway... that's just my $0.02.