4 Runner hands down.

newer explorers are having tranny and differential problems, and there is no
way to know if you are buying one that will have problems.

There is a reason they are referred to as Exploders

Aside from the fact that you're trying to compare apples and oranges.... Job
2 Explorers in our area have been relatively trouble free.... There are NO
4Runners in our area....

Interesting point.... Fords concerns seem to be well known.... kinda like
saying "we know there is a concern and we ae working to a resolution...."
unlike other marques that downplay just about anything.

Good luck with your decision.....

I faced a similar dilemna and picked a 2002 Explorer. Although Toyota
as a brand still owns the overall 'quality' crown, the gap between
North American and Japanese has narrowed substantially over the past
few years.

A few things to note:
1. starting with the 2002 model year the Explorer has better crash test
and safety ratings than a 4Runner according to the NHTSA.
2. Explorers depreciate more quickly (north american, # on the road) so
you'll get more truck for your $ if buying used.
3. Any differences in fuel economy between 4Runner and Explorer will be
made up for in savings for insurance (YMMV).

In the end I got a 2002 Explorer XLT fully loaded w/ 80k km, with an
extended warranty (3 years) since it was coming off of lease, for
several thousand less than the average price of a 2000 4Runner. I
bought the ext warranty out of fear of murphy's law, but haven't needed
it within the first 6 months.

My daughter looked at buying a 98 or 99 4-Runner 2 years ago and the dealer
was just way too proud of it.  Way too many miles and wanted much more than
retail.  She ended up buying a 2000 Grand Cherokee with half the miles for
less money.  Her car has been about as reliable as my 2000 Explorer XLT was.
I bought it with 25k miles on it and just traded for a new Sport Trac with
78k miles.  The only problems I had were drivers power lock broke and back
door latch on inside broke.  17 mpg city and 22 mpg hwy.

I had a 4runner for 4 years.  Not a single repair other than brakes.  Needed
new tires but lease ended and I did not replace them.  Wanted to get the
Sequoia for the 3rd row seat but was concerned about gas mileage.  Sooooo - I
bought a 2004 Explorer XLT.  Found out right away that the gas mileage in the
Explorer was about the same as the Sequoia.  And - I am researching lemon
laws as we speak.  I have had nothing but repeated transmission problems with
the Explorer.  Right now they are trying to fix a stalling problem and a lag
when you give it gas as you turn a corner.  I am reading a lot of entries on
various websites with similiar transmission problems.  Also had recall
problem with harsh reverse.  Had problem with coasting through parking lot
and then when applying gas you get lurched forward.  There is a weird
skipping from the tires when you first start when making a 90 degree turn.  I
have seen all these problems posted with the exception of random stalling.

Hands down better gas mileage and fewer transmission problems with 4runner.
Hope it's not too late.