Lots of guys here share the opinion that if you re-gear, go 4.88 or 5.29. This also allows you to go bigger on tires in the future and have decent gearing, good if it might be a trail rig in the future.
Also, 4.10 and 4.30 are the common ratios for 4runners, so if you end up having to replace something in the future, a 4.1 or 4.3 will be alot easier to find than a 4.56.
To me, 4.56 wouldn't be an option because it just doesn't seem to be very common. If you want to gear up a bit lower than 3.9, then I'd say go for 4.88, but if you are afraid of that low a gearing, see if you could find a steal on salvage 4.3's. You could possibly get them for super cheap if you are patient. Most guys here will probably say that won't make a noticable difference going from 3.9 to 4.3, but you could find 4.3's with a locker, which is another big plus.