I've used CLR to unblock a clogged heater core. It's not exactly cooling system friendly, so you really want to keep it there for as short as possible.
For it to work properly, you will first need to flush the system so there is no coolant left in there, just plain water. Then wait for the engine to cool down a bit, and add the whole bottle of CLR.
Because CLR foams, you want to keep the radiator cap off. Turn on your heater, and let the engine idle with the rad cap off until the thermostat opens. Once it does, get the thermostat out and start thoroughly flushing the system.