Question

What are the largest organizations that are focused on marine conservation, and who funds them?

Answer 1

I am not sure who funds all of them but these are the ones that came to mind, there are hundreds.

NOAA

SURFRIDER FOUNDATION

ONE WORLD ONE OCEAN

REEF CHECK

THE OCEAN PROJECT

Answer 2

Well, here are a few sources of names of orgs. Their funding sources likely vary.

https://www.scubadiving.com/marine-conservation/list-non-profits-focused-marine-conservation

http://www.motherjones.com/environment/2006/03/guide-environmental-non-profits/

I recommend cross checking against a vetting org like Charity Navigator.