FLC OF AN LGT WARNED OF LOW ALT DURING A VOR APCH USING LEAD-IN LIGHTS FOR THE LAST SEGMENT.

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THE NY METRO AREA HAD QUITE A BIT OF TSTM ACTIVITY IN THE AREA. JFK WAS USING THE CRI VOR APCHS TO RWY 13L. AS WE APCHED THE CRI VOR; NY TRACON ADVISED US WE WERE CLRED FOR THE APCH; AND TO CROSS THE CRI VOR AT 1000 FT; WHICH WE DID. THERE WAS A RATHER NASTY TSTM JUST W OF THE APCH PATH. AFTER WE PASSED THE VOR; WE STARTED A NORMAL DSCNT FOR THE ARPT AND PICKED UP THE LEAD-IN LIGHTS FOR RWY 13L AT JFK. ABOUT HALF WAY BTWN THE VOR AND THE FIRST LEAD-IN LIGHT; THE CLOUDS FROM THE BASES OF THE TSTM APPEARED TO BE SLIGHTLY BELOW OUR 800 FT NORMAL ALT. I MIGHT NOTE HERE THAT THE APCH CHART GIVES NO SUGGESTED ALTS OR ALT RESTRS ONCE THE APCH LIGHTS HAVE BEEN SIGHTED. WE HAD A GOOD VISUAL ON BOTH THE APCH LIGHTS AND RWY AFTER LEAVING THE VOR AND UPON REACHING 800 FT. I FELT BOTH THE FLT AND ALT WERE SAFE. WHEN IT SEEMED WE MIGHT LOSE SIGHT OF BOTH RWY AND LEAD-IN LIGHTS IF WE STAYED AT 800 FT ALL THE WAY AROUND TO FINAL; WHICH JFK LIKES FOR YOU TO DO FOR NOISE; THE FO STARTED A SLIGHT DSCNT TO MAINTAIN THE MAX POSSIBLE ALT AND KEEP BOTH RWY AND LEAD-IN LIGHTS IN SIGHT. AS WE STARTED OUR TURN FOR THE ARPT; THE TWR CTLR VOICED SOME CONCERN THAT WE WERE INDICATING AN ALT OF 450 FT AT THAT TIME. I TOLD HIM OF THE LOWER CLOUDS TO THE W; AND HE SAID THEY WERE CHANGING THE APCH TO RWY 22 AS WE WERE SPEAKING. I TOLD HIM THAT WE WERE FINE AND THAT WE HAD BOTH THE LIGHTS AND RWY IN SIGHT. I ASKED IF WE WERE CAUSING A PROB; AND HE RESPONDED WITH SOMETHING LIKE; 'NO; I WAS JUST CONCERNED BECAUSE YOU WERE BELOW THE NORMAL ALT.' WE CONTINUED THE APCH AND LANDED ON RWY 13L WITH NO PROB. I WAS JUST CONCERNED THAT HE QUESTIONED WHAT WE WERE DOING AT THE TIME.