Could be sway bar/end links as suggested above. Takes about 15 minutes to remove the sway bar completely, I'd try that to rule it out.
I've also had a rattle caused by worn out m-springs on the front brake pads. Every time I went over a big bump the pads would rattle loudly and it sounded like my front end was going to explode. New m-springs and some brake grease on the slide pins is all it took to fix (about 3 dollars in parts and 1/2 hr of time).
I don't think you should trade the 4runner in because of a small rattle and other little issues you've had with it. I know you want your truck to be perfect and problem-free, but I think you might have unrealistically high expectations. Every vehicle you own is going to have a set of issues that crop up over a period of time, doesn't matter if it's a 4runner or a $60k Benz. Sometimes things start rattling and need to be fixed, such is life.
But if you want a different ride altogether, by all means trade it in. I don't think you'll get any less money for it because of the rattle. I traded in my Volvo S60R for the 4Runner and it had blown spring seats and failing shocks. It rattled like hell and clunked over every bump, but the dealership didn't even test drive it, they just gave me essentially what I wanted for it. Dealerships usually just wholesale their trade-ins at auction anyways.
