It happened just before 10 p.m. at the restaurant at 2516 White Plains Rd.
The video shows the suspect walking into the store, exchanging words with the two boys before firing at least six shots.
Based on the video, the boys appear to be the intended targets, although the motive is unclear.
A 12-year-old boy was struck in his back and left leg. The 13-year-old was shot in the left thigh.
Both are stable at Jacobi Hospital.
Police say the suspect ran away on Mace Avenue toward Bronx Park East.
The suspect was last seen wearing a blue medical mask and a black hoodie with a pink logo on it.
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