It is undetermined at this point, but I think that with a project of this magnitude and given the scope of its significance across the Great Lakes.... Really, this is very much in the interest of the Mississippi River communities as well, because far more invasive species have gone from the Great Lakes to the Mississippi than have gone the other direction.
A combination of federal, state, and local funding would probably be necessary to make this a reality. The other possibility is some public-private financing in connection with transportation upgrades that would be done. It seems that with something of this nature, spreading it out as much as possible would be the most advisable way to go.