I'll throw in my .02 and another vote for the Sequoia. I was in a similar situation about 2 years ago when we picked up our '06 Limited.
My wife's criteria were that it had to be comfortable for road trips and have a 3rd row seat for we we visited family. My additional requirements were that it had to be able to tow at least 5000lbs and be 4wd, with my preference being Toyota and $10k or less.
We looked at 4th gen 4runners and found them to be:
A. Too small
B. Finding one with a 3rd row seat in our price range was next to impossible.
C. Most expensive than a comparable Sequoia.
We also looked long and hard at '98-02 100 series but again finding one in our price range that wasn't trashed proved to be difficult. We did eventually find a very nice '99 for sale locally that we test drove, and that is were we ran into the other issue...it was just too small for what we intended to use it for. Which was saying something as this was going to be a replacement for my '95 4Runner that I had at the time.
It was then that we narrowed our search down to the Sequoia and then the hunt was on to find the "right" one. After several evenings of research I had narrowed my search down to '05-07's for the following reasons.
A. 4.7L w/VVT - more power for towing
B. 5-speed A750F transmission
In the end we found a '06 Limited ~2hr north of us for $10k, it had ~198k mi on it but it had a full service history from the 2 previous owners and had either been serviced at the original dealership it was sold at or a local toyota mechanic. Also adding to that were receipts that the timing belt/water pump had just been replaced with toyota/aisin parts.
So far it has never let us down, and we've put ~30k on it since purchase. That only failure that we've had so far is the dealer installed DVD player died about 6mo ago, but that's no fault of the truck. It is by far the nicest road trip vehicle I've ever driven, and eats up the miles easily, including two family trips to WI this year (1500mi one way) and several shorter trips to northern New Mexico (9hrs one way). Offroad wise it has easily handled forrest service roads in Southern Colorado along with making it over Cinnamon Pass in between Silverton & Lake City without much trouble, mind you mine is bone stock with the exception of some Toyo Open Country HT tires. All in all it has been the perfect rig for our needs and we plan on keeping it until it dies.