WDB ON DEP VECTOR WAS PUT IN CLOSE PROX TO AN ARRIVING WDB WITH LESS THAN STANDARD SEPARATION.

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DEPARTING JFK ON RWY 13L; GIVEN KENNEDY 1 DEP WITH A 090 DEG HDG AFTER DEP AND CONTACTING DEP WE WERE GIVEN A 110 DEG HDG AND A CLB TO 6000'. TFC VFR SMA Y 10-11 O'CLOCK; 4500'; SWBND. I RESPONDED TO CLRNC TO 6000' AND RIGHT TO 110 DEG HDG WITH THE SMA Y IN SIGHT (THE SMA Y TURNED ON ITS LNDG LIGHTS WHEN DEP CALLED TFC; ADDING CONFIRMATION). WE CONTINUED TO 6000'; KEEPING THE SMA Y IN SIGHT WHEN DEP CALLED LEFT TO 360 DEG HDG; TFC 12 O'CLOCK SBND WDB Z. WE BOTH TOOK OUR ATTN/EYES FROM THE SMA Y (NOW 10 O'CLOCK) AND SAW THE WDB Z AT 1 O'CLOCK BELOW OUR ALT SBND. TURN WAS STARTED AND I RESPONDED; TFC IN SIGHT; LEFT TO N. I BELIEVE THE WDB Z WAS ON APCH FREQ AND WAS IN AND OUT OF THE CLOUDS/BASES. FURTHER CLB WAS GIVEN WITH A HDG OF 020 DEGS TO INTERCEPT THE 065 DEG R OF JFK VOR WITH NO FURTHER MENTION OF THE REDUCED SEP OR CAUSE/BLAME OF PROB. IN MY EXPERIENCE; USUALLY OUT OF JFK TO THE E; ONE GETS A HDG OF 020 DEGS TO INTERCEPT THE 065 DEG R JFK VOR ON CONTACT WITH DEP. GOING FURTHER E ON DEP IS NOT COMMON DUE TO IFR ARRS. NOTE: FIRST FIX AFTER DEP WAS CHECK; WHICH IS TO THE N.