Regarding the cemataries near JFK, departing flights veer off long before reaching the cemetaries. and arriving flights generally don’t use the runways in line with the cemetaries. Use of runways 13L and 13R (whose approach is over a number of non-denominational cemetaries) would conflict with LGAs runway 4 and runway 22R (Whose approach is over Montefiore Cemetary) is normally used as runway 4L.
Mount Zion Cemetary is not in line with LGA’s runway 4 (but it is possible that an approaching plane will fly over it).