First of all, DON'T take the new Sudafed PE, or anything with phenylephrine. My doctor, who's very much a traditionalist about throwing medicine at illnesses, says the new product just doesn't work well enough to be worth taking... and in my experience I agree with him.
The original Sudafed - pseudoephedrine - does work, but you probably have to get your doctor to write you a prescription for it, since it's no longer over-the-counter. Never heard about it affecting milk supply, though.
My favorite remedies are the old-fashioned ones that don't involve pills. Vicks VapoRub or something similar rubbed on your chest. A few drops of Olba's Oil in a bowl of steaming water. Put your head over the bowl with a towel over your head to create a "steam tent". No "medicine", no risk to you or baby, and it works to clear your sinuses.
Good luck!