I think the heater core is fine on the 4th gen. 4-runner. Mine pumps out heat great.
Some recomendations though -
The 4-runner doesn't come up to normal operating temps when it's zero or less out, I can tell this by noting the needle's position on the temp. gauge. Until you are driving the 4-Runner on the highway, where you are *pushing* the engine a bit harder than just in-town driving, the engine (V6 in my case) isn't generating a lot of heat relative to the heat it's losing through the engine compartment and radiator. Once on the highway though, the needle moves to the normal position and there's an abundant amount of heat available.
If you are having trouble with heat, for the short term periods, I'd drop the gear down into 4 or 3, depending on your tranny, causing the engine to run at higher RPM's. This will help bring the engine up to temp. quicker.
Carboard over the radiator is good idea too. Take the time to secure it properly though, and it doesn't have to cover every little bit of it either, just the majority to make a difference.
Recirc was already mentioned, but that will help too.