There used to be a woman on here with the name "Montezuma" who gave great advice on whooping cough. Maybe do a search. I don't believe she is on the forum anymore, but I believe her old posts can still be found and are very detailed and helpful.
Also, sodium asorbate is supposed to be great. It's a form of buffered vitamin C and comes in powder. You will probably have to special order this stuff, as I've found most health food stores don't always have it. Do a search on here and you can find some good threads for it's use. It's supposed to lessen the symptoms of whooping cough. Keep breastfeeding and make sure your baby is propped up while sleeping.
if you don't have a homeopath, the book Smart Medicine for a Healthier Child lists good homeopathic remedies for whooping cough.
Also our pediatrician sees a few cases of this per year and uses nebulizers and singulair (don't know if your baby is too young for these). But I read somewhere on here from an adult that had WC that she didn't feel better until she did a nebulizer. I'm not a big fan of nebulizers, but it might be helpful is the sodium abscorbate and homeopathic remedies don't work - which I have read on here for some it works wonders and for some it hasn't helped much.