I am no medical expert, but I think the main concern is whether or not the wisdom teeth present a significant risk of becoming a future problem, either during BCT or the academic year. I didn't have mine removed beforehand because my home dentist thought issues with them were unlikely in the near future, and that I could just as easily have them removed a year or so later. I ended up getting them out after finals during spring of my 4* year.
I should also add that recovery time will almost certainly be easier to handle if the surgery is performed prior to the Academy. In my case, I had somewhere around 2-3 weeks of time to heal before heading right into ESET (survival training summer program). I was fine with that, but the close proximity of other events (classes, airfield duties, etc.) makes the surgery harder to fit into cadet schedules. No regrets from my perspective, but definitely something to be aware of.