If you have the original wheels on your '04 Limited, they should be a machined finish aluminum wheel with a clearcoat finish on them.
You shouldn't be seeing black at all, even if the clearcoat is blistering and peeling. I've seen that happen to wheels when people use the wrong type of wheel cleaner on their wheels.
If your 4Runner is no longer in warranty (probably the case with a 2004) then you'll either have to replace the wheels (expensive) or have them refinished by a reputable wheel refinisher.
Your best bet is probably looking for a set of used wheels on ebay.