I am not sure what exact your situation is, but based on what I know, these three majors are very similar. I presume that the major course requirements are also similar. If you are interested in the one that may yield better job prospect, I would recommend you choose the major that is under engineering department.
I am not a medical student, but based on the background of MD/PhD students that I know of, major has little impact on whether you can get into a program. Indeed one MD did comment on that major didn't have much impact on whether you can go to a medical school. Your GPA and the institute may have greater impact. Knowing the faculty of the institute of your interest is also important.
To sum up, I am not sure whether these three different majors would make much difference. However, I would suggest you to look for summer research internships in the institutes that you want to. Making people know you will increase your chance. Also I am not sure whether you have entertained the idea of getting a MD/PhD. The PhD will pay for the MD.
I hope all these help. Good luck!