At around 5 a.m., two men entered the Chabad Synagogue Beth Menachem Mendel located at 1703 Avenue J in Midwood.
Once the suspects were inside, they awoke a 53-year-old man on the third floor and hit him with a rotary cultivator garden tool over his face and head, police say.
The suspects fled through the rear door with a laptop, cellphone and the victim's wallet with approximately $300 and credit cards. Police say he also stole donations that were meant to be given to charity.
The victim was taken to Maimonides Medical Center.