The break-in happened at around 4 a.m. Tuesday at the store in Gateway Plaza in East New York.
The burglars broke the front glass doors and pried open the security gate.
They then broke into two security cages in the manager's office where the Apple tablets were being stored.
The stolen iPads are worth a total of $112,000.
Some of the security cameras in the store weren't working at the time, but police are going through the ones that were.