To me, that's like asking 'which one of your kids do you like the most?'
They are both good rigs with positive attributes but are different in size and capabilty.
The 100 is bigger, more comfortable, especially for a larger guy like me. I have a 2000 100 series and the seats are far and away the most comfortable of any car I've owned. On the downside, the 100 is a BIG car, much less nimble on tight trails, although the 100 is not my trail truck.
The 4runner is smaller, more nimble, better fuel economy, but carries less and is less powerful, unless you find one with the 2UZ V8 which is definitely the sweet spot of 4Runners.
Year to year, the 100 will cost you more up front and probably all the way along, but will be worth more when you're ready to sell it.
g'luck. Dan.