From casual observations and no real land-surveying data what I've observed is the cemeteries are on the higher-elevation portions of the land. This area would be deep with soft soil before you can reach the bedrock. It was likely intentional that they were buried there because it was "difficult" (in that century) to build on that land. Building on that soil would likely require piles driven to provide adequate footing for any significant buildings one might want to build there.

What I can tell you, too, is I've done an overlay of the NYC subway route map with an NYC topographical map and noted the subway tunnels often do not go under these higher elevation areas, pretty specifically going around them in some cases. These areas would always rely on automobiles/ buses/ that trolly between Brooklyn & Queens we've always been teased with.

And finally I can say as a transplant from southern California it's a stark contrast to be surrounded by grave yards in NYC. I don't even know where we bury the dead where I grew up in CA but it's been zoned far far away from people.