It sounds like you may have low coolant in your engine, or a large air bubble that is preventing proper circulation of the coolant through the radiator and heater core. It is a fact that when coolant level falls, the heater core is among the first components to be starved of flow. So, whenever heat is good, then cool, suspect low coolant level.
These engines are prone to air blockage if they are not filled with coolant properly after the system has been opened. Part of the problem is the solid flange on the thermostat that does not allow trapped air out of the engine. The fix for this is to drill a small hole 1/16" or 3/32" through the flange as an air bleed and install the thermostat so that the hole is at the highest point.
How you refill the cooling system makes a lot of difference. Basically, you want to fill the engine at the thermostat opening, then fill the radiator with the thermostat out until coolant overflows at the thermostat opening. That will prevent big air voids in the engine that may be causing your problem.
Read a detailed procedure for refilling here: http://www.bonnevilleclub.com/forum/...=article&k=100