From what I researched when my oldest had a really bad case of croup...
Croup is a symptom, not a disease, like runny nose or fever. Specifically it is a swelling of the larynx which causes a narrowing of the airway. In adults it usually just causes a sore throat. In young children, because the airway is small to begin with, even a small swelling can make it harder for air to pass through. It usually causes a cough like a barking seal. In worse cases it causes stridor which is a noise that you hear when they breathe in (as opposed to wheezing which is noise on exhale). In really serious cases it can obstruct the airway enough to cause respiratory distress.
There are certain viruses that are more likely to cause croup, but really any upper respiratory virus can cause it. Some kids are more prone to it and will tend to get it with almost every cold, others will never get it. Mild cases to moderate cases are usually treated with humid air (think steamy shower). More serious cases can require more intervention. Now, this doesn't mean that every doctor will use the term 'croup' correctly, but this is how it should be used.
Whooping cough, on the other hand, causes uncontrollable fits of coughing, but it is just regular old coughing, not the barking cough of croup. It comes from deeper down in the lungs - croup is up in the throat. I have had both and can tell you that they not the same.
Again, doesn't mean the ped is correct, but they aren't the same.
One last point - if your SIL's boy has been exposed to CP make sure they do not treat him with steriods for the croup. Some peds will jump in with the steroids at the littlest sign of croup instead of saving them for the really serious cases. We all know that steroids and CP don't mix.