I can clarify this one a bit - I've seen the 'glass bottom' boat at Nassau. I'd never go on it. Like the above poster said, It's a double decker boat, with some small viewing windows on the lower deck facing down. The viewing area appears very limited.
What you want to look for, and I think only St. Maarten currently has any(anyone correct me if I'm wrong), are called semi-submersibles. We took one of these on St.Maarten on the 7 day Eastern. The entire compliment goes below on benches with windows about 2 foot square covering both sides. Absolutely wonderful unobstructed views.
In Nassau, If you want to see unbelievable sea life, go to Atlantis. I have directions posted on this board, titled 'Atlantis Info/Pricing Inside'. You will not be disappointed.