What is the best way to photograph underwater through a glass?

The answer, of course, depends on which camera you are using, what objects you'll photograph, and the desired style of your photo.

Style:

Let's start with style of photo first. If you want a wider angle, curved view, fisheye look, you'll want a fisheye lens. If not, you'll select a rectilinear lens. Some fisheye lenses can capture 180 degree field of view and distort the image. If you're taking a picture of a single shark, for example, a fisheye lens may not produce the most pleasing image.

Objects:

If shooting large aquatic animals, you'll typically want a rectilinear zoom lens. Because it's difficult to obtain quality photographs from a distance underwater, the focal length will still be fairly short, usually less than 24mm. For smaller objects, you'll typically want shorter focal lengths.

Camera:

Canon and Nikon have Excellent lens choices, but third party lens manufacturers also make great lenses, but are typically less expense. Here's a good lens list for Nikon and Canon:

For Nikon:

Fisheye:

Nikon 10.5mm (cropped sensor)

Tokina 10-17mm (cropped sensor)

Rectilinear:

Nikon 10-24mm (cropped sensor)

Nikon 12-24mm (cropped sensor)

Sigma 8-16mm (cropped sensor)

Tokina 12-24mm (cropped sensor)

For Canon:

Fisheye:

Canon 15mm

Sigma 15mm

Tokina 10-17mm (cropped sensor)

Rectilinear:

Canon 10-22mm (cropped sensor)

Sigma 10-20mm

Sigma 8-16mm (cropped sensor)

Tokina 12-24mm (cropped sensor)