Do not stop nursing. Doctors ALWAYS say this and it is not right. Tummy troubles can cause temporary sensitivity to milk but breast milk is not the same and it has antibodies to help him fight whatever he has. I would just nurse and if he throws that up (it's ok if he does) nurse some more and you can give some water or pedialyte with a dropper, just small amounts occasionally to make sure he stays hydrated. You can sleep with him in your bed tonight and lay down several layers of towels on the bed. That way if he throws up, you can just peel off a towel or two and lay down on the one underneath, or get a clean one. It will be a long night though. Ear can have fluid without it being an infection...sounds like he might have something else....stomach virus or something. I would also wait the 4 - 6 hours and try giving him some tylenol or ibuprofen again to keep the fever down. If it is a virus, the dr. won't be able to help much anyway and they will just tell you to keep him hydrated and to trade off giving tylenol and ibuprofen every 4-6 hours to manage the fever. I would make an appt for tomorrow with your reg dr. though just to make sure.
I know high fevers and projectile vomiting are very scary, but they are not uncommon even with viruses. If you think the antibiotic is making him sick, I wouldn't give him anymore, just manage the fever and liquids and get in to see your reg dr. asap tomorrow.