We have both
We currently have a 3rd gen. 1997 2WD Limited 4Runner and a 1st gen. 2002 4x4 Sequoia Limited. Here's my take on them:
Reliability:
Tie
The only major problems we've had were due to auto trans failing on both and having the dealer put in a reman on the Sequoia around 75,000 miles and the 4Runner's tranny was rebuilt around 115,000 miles. I do attribute the failures to inadequate ATF fluid replacement.
Ride Comfort:
Sequoia is the perfect road tripper. It sucks gas, about 18 mpg highway, but it's ultra smooth and comfortable when driving for 1,000s of miles.
Safety:
Sequoia with all its front and side airbags, 4WD option, larger mass, and good visibility from the driver's seat.
Driveability:
The 4Runner is absolutely more fun to drive for spirited, WOT runs on the highway and has a sportier feel. The Sequoia although large is still quite agile but the driving feel is more numb.
Top speed that I have attained on abandoned coal mining roads:
3.4L 4Runner 108mph
4.7L Sequoia 103 mph (before governor kicked in)
History:
The 4Runner/Hilux has a revered history globally.
The Sequoia looks to be discontinued in the near future.
What I want to drive to my grave: 4Runner (or a Land Cruiser)