Sage,

I've removed water from under glass before with a shop vac.

Cut away some of the glass on the deck but don't go larger than the shop vac's hose diameter. Now, mark the area that is affected by drawing a circle around it in wax pencil (or any other removable marker) Carefully drill around the outside of the the marked area and through the deck glass and into the wood with a small bit. Apply the shop vac to the larger opening making sure you have a good seal to the hull surface.

Let it sit that way for a couple of hours with the motor running.

Eventually, all the water will migrate to the vac opening and out of the wood.

Reseal the drilled openings, fashion a glass/epoxy patch (lots of directions for this procedure on this forum) and you've got your fix.

You may not be able to get the stain removed unless you're willing to also cut away the darkened area and patch that section of the wood as well.

Good Luck,

Chris