[stugiv]

Make sure that you know for sure whether the leak is between the plexiglas and its frame or if its leaking around the hatch base itself.

I re-bedded the plexiglas into a frame many years ago on a Sea Ray. It was pretty simple, I used a black adhesive caulk which I think was 3m 4000. Of course, you'll want to clean the area as best as you can before re-bedding & then clean up any excess before it dries.