We have the luxury of owning a 18' 4runner ltd and an 18' highlander ltd... I have 2 daughters (4 yr and 1 month). The highlander is the DD and the 4runner is strictly a toy for road trips, 4 wheeling, weekend running, and occasionally gets driven to work on nice days. If I had to choose one over the other it would be the highlander.... this isn't to say I don't love our 4runner though. The highlander has better safety features, a better crash test rating, and is just more practical than the 4runner. The rear HVAC and controls is significantly nicer on the highlander as well... you will get ventilation to the 3rd row whereas I don't think you do on the 4runner even with a 3rd row option.

This is with 2 kids... 3 to me is a no brainer. BUT I would be lying if I said the highlander 3rd row was spacious with the second row at a reasonable seat back/leg position. A 10 yr old may be cramped in the back so one of the 6 yr would have to ride back there I'd think. Are your 6 year olds still in a booster? (sorry if I missed that).