My 1 year old has an ear infection and is on amoxicillin, this morning when he woke up he was burning up with a fever and threw up, what should I do?

See a doctor. It seems like your child is not responding to the antibiotics and i would recommend that his doctor see him as soon as possible. You want to make sure this simple ear infection doesn't become anything more complex.
Resistant infection. Your son probably has a germ that is not responding to this antibiotic. You should have him see his doctor again.