I know this advice will not set well with many, but this is what I know, so here goes!
Your son is three years old now. It is important that you teach him now that you love him, and that you make all decisions based on what you know to be best for him. That he is to do as you ask, because it is what is best. He needs to learn that sometimes you may ask him to do something that he doesn't want to do, but for his own good, he needs to do it anyway. He will need this skill of submission throughout his life. If he doesn't learn it at an early age, you will have a very tough row to hoe. Imagine him, 12 years from now. Do you want him to listen to you because you know what is best and you want him to trust you, respect you, and obey? Or do you want to have to convince him as to why you feel the way you do, and hope and pray that he agrees and listens to your advice? He will also need submission skills in the work force. You won't want a son that can't hold a job, that quits because the boss wanted him to do something that he didn't want to do. I know it may sound silly, projecting that far in the future, but he is learning skills and attitudes now that will affect the rest of his life, and it all starts somewhere!
I would suggest that you purchase medicine that doesn't taste bad. Make sure hold him on your lap (you don’t want to be chasing him around the house with a bottle and a spoon!) Tell him that it is time to take his medicine, and that it will help him get better. If he says he doesn’t like medicine, tell him you know, but that you love medicine because you love him, and it will make him better. If he refuses to take it, give him a little flick on the mouth with your index finger. CALMLY repeat the instruction that it is time to take his medicine, keep doing this until he obeys. Remain calm, do not under any circumstances, raise your voice. It may take awhile, if submitting is a new skill for him, but he will come to understand that an undesirable behavior reaps undesirable rewards. When he is finished taking his medicine, tell him he is a good boy and give him a love!