I believe (sure someone will correct me if I'm wrong) that plebes are permitted to bring with them a pair of broken-in running shoes. Thus, focus on finding a pair that is comfortable.
Agree with those above that it is much better to focus on being in shape than in running in combat boots. You never have to do that for USNA purposes. As noted, if you decide to go SEAL or maybe if you do jump training, you may need to run in boots. However, that doesn't happen as a plebe and, as also noted above, they'll issue you a pair when the time comes.
You really want to avoid injuring yourself before plebe summer. If you can't participate in plebe summer (i.e., have a broken leg), they may well send you home. Thus, try to avoid any type of "risky" activity where injury is likely -- and that includes running in combat boots.