Three prolific thieves suspected of knocking off 31 top jewelry and accessory stores were busted early yesterday while allegedly breaking into a Brooklyn boutique — for the second time.

Major Case Squad cops had Elleven Jewelry on Court Street in Cobble Hill under surveillance when they spotted two men in front at around 4:45 a.m., said owner Nasim Cohen.

They allegedly swiped $50,000 worth of swag and were walking to a nearby getaway car and driver when cops pounced, sources said.

“The detective . . . said, ‘We got the bastards. We have your merchandise. Don’t worry.’ ” Cohen said.

The men allegedly started their spree in October.

Busted were Carlos Ortiz, 37, of Brooklyn; Anibal Cruz, 25, of The Bronx; and Ricardo Acevedo, 45, of Queens.

All have lengthy rap sheets. Cruz and Acevedo have burglary arrests from the past decade.