Unless you're planning a long travel front end, go stock.
While I generally agree with what COB said, I've seen some Tacomas & 4Runners with stock width suspension and spacers that look pretty good. I know that I've seen some 2000-2006 model Tundras with a simulated flare molded into the front fender, and it looked Badass.
It would be pretty cool to see a 4Runner with a DIY flare painted on with Berliner or something. I think it would all depend on the style of fender you get. Hannemann, Glassworks, Fiberwerx, etc all look slightly different. Just make sure that you don't get any thing wider than a 3.5" flare, or it won't look right.
There was a company called Boatec (sp?) that made a "close to factory" fender that would probably look the cleanest on a rig with stock width suspension. I think the flare was slightly narrower too, around 2.5" or something.
Just remember, fiberglass fenders come out of molds that aren't perfect, so generally speaking you have to do some trimming to get them to fit right, especially around the corner markers. After that you'd need to paint them too. But even paint's optional IMO with a white rig because the fenders come with a gel coat that's kinda glossy, and it matches the paint decent.
Just a couple of things to take into consideration, but if done right will look good, not to mention there's not a lot of 4Runners set up like that so it would be kinda unique. I say go for it!!!