Since the sound from the CD player is unaffected, I think you're right in suspecting something with the RF portion of the head unit.
What exactly do you mean by "then you can hear what sounds like a speaker coming in and out" ? Are you talking about feedback or signal fade ?
There are lots of things that could interfere with a radio signal, so having an idea of when it's happening and if it does so in a predictable manner is pretty important. When does it happen ? Is it at a particular place on the road or just sitting in your driveway ? How long has it been doing this ? Is it a recent development or not ? What bands are affected (AM, FM, WB) ?
Think about these questions to narrow down the possible causes. Here are a few things I would do in terms of troubleshooting. First, I would first check the antenna connections, one at the back of the head and the other where the antenna cable connects to the antenna. You might have corrosion in either place, but particularly in the wheel well where the antenna is located. Second, if you have a portable radio, take that in the truck and see if it reacts the same way when the radio in your head unit is acting up. If it does, then it's likely an RF interference problem.
Lastly, if you have a microwave oven installed in your truck, I would suspect that might be the cause of your problem
Kev