1996 Chevy Suburban Heater not putting out enough heat

I recently had the engine replaced with a remanufactured, warranteed engine. Before the engine was replaced the heater worked great. Now it doesn't produce enough heat at the heater vents. I took it in to the shop that did the engine work and they put a higher temp thermostat in but it still isn't working right. When I am driving if I accelerate the heater puts out plenty of heat but only for a few seconds. The shop recommended replacing the heater core but it seems to have enough hot water in it.