Lack of cross flow ventilation is why Mainship Pilots and downeaster style boats in general are popular in New England and less so in the south. At anchor, ventilation is no problem, because the bow is always pointing into the wind and the big central opening window and the two overheads provide lots of air.
But at the dock where the wind direction is probably not coming from the bow, ventilation in the bridge deck area is limited. Older, roughly 2000-2006 Pilots have Stratiglass side windows and some have U-shaped cutouts to allow cross ventilation. When we bought ours several years ago, it had the U cutouts, but when we replaced them a few years ago, I decided not to add the cutouts as we use the boat in LI Sound and it is ok without.
Fans in the overhead as Don notes above could certainly help. You should be able to snake power up from the DC panel to the little cutouts, but I haven't tried that myself.