Wow, I posted the exact same topic about a month ago! My pup Nigel had a swollen lymph node on the back of his hind leg (the popliteal lymph node), which I finally figured out was because of a toenail injury he had. Nigel's lymph node was about the size of a grape. It went down completely on its own over the next 4 or 5 days after I noticed it. If your vet gave you antibiotics I would think you have nothing to worry about. Are you sure your dog is whining because of the lymph node? When Nigel's was swollen I don't think he really felt any pain, or at least he didn't act like it.
If you research "swollen popliteal lymph node" on google you will find some information, mostly pertaining to humans but it is still useful. Good luck and I hope you feel better and your dog feels better very soon!