In terms of the application, no one here can really say definitively how choosing bio over physics would affect your acceptance.
On the other hand, choosing one or the other could set you up for an easier time down the road, depending on which program you wish to pursue at the Academy. Check out the USAFA core curriculum,
https://www.usafa.edu/app/uploads/Core_-Curriculum_Chart.pdf.
Cadets must take Physics 110 and then any 2 of the following classes Physics 215, Bio 215, and Chem 200.
Now, here is a list of all the courses that can be waived with AP test scores (at the bottom),
https://www.academyadmissions.com/the-experience/academics/grading/.
(Actually, looking over this list, I'm fairly certain they've got the physics waiver requirements between 110 and 215 switched. Also, it says you can apply AP credit to Bio 315. Bio 315 is the same as Bio 215. It used to be a 300 level core course and the AP list has not yet been updated to reflect the shift to the 200 level.)
I'm not sure how AP Physics courses work, but if you can somehow knock out both AP Physics C Mech and AP Physics C Elec/Mag, then you will save yourself from two courses. If you take AP Bio, then you can at best test out of one course. In the time that I was at the Academy, core bio was WAY easier than core physics. Take that as you will.
One last thing, cadets who have declared a major will typically take a special intro class in their declared major that replaces the matching core requirement. As an example, aero majors would take Aero Engr 200 earlier and not need to take core Aero Engr 315 later. From my experience, this intro class for declared majors cannot be waived by AP scores. So if you wanted to major in Bio, you could not waive the intro to bio course for bio majors even though you could waive the core bio course. I don't think the physics department runs an intro to physics course for physics majors.
I'm sorry if I've given you way too much info that wasn't really pertinent to your original question. Good luck!