Bayonne is sheltered by Staten island, not as exposed to direct ocean wind. Also low elevations all around Bayonne so the wind carries over the land. Downtown JC has high elevations on the west so the wind gets trapped. Hoboken is actually worse with regard to bathtub affect (it's why flooding is worse, because the western part of Hoboken actually goes down in elevation), but further up the river so less wind.

Also not based on science.