My son has been sick for 5 days with aching legs, headache, fever and upset stomach. He is also getting congested in the head. Could this be the flu?

Yes. Influenza is widespread right now, so the constellaton of symptoms you descibe certianly could be influenza. Could also be other viruses or strep, so best to have child tested to see what is what so appropriate therapy can be initiated. Drink lots of fluids and rest!