Which corporation has operational control over the waters of Lake Ontario?

The St. Lawrence Seaway Development Corporation is responsible for managing and maintaining the navigation facilities of the St. Lawrence Seaway, which includes controlling access to the waters of Lake Ontario. This corporation ensures that the shipping lanes are safe and navigable, thereby playing a critical role in controlling the waterway's operational aspects. As part of the broader St. Lawrence Seaway system, it coordinates with various stakeholders to facilitate commercial shipping and manage water levels, further demonstrating its comprehensive control over operations affecting Lake Ontario.

The other organizations listed may have roles in areas related to shipping, logistics, or port management, but they don't hold the overarching operational control over the navigational and infrastructural components of Lake Ontario as administered through the St. Lawrence Seaway.