Waterfront of Tomorrow Act of 2013 - Directs the Secretary of the Army, acting through the Chief of Engineers, to study measures that provide the greatest flood protection and climate resilience for New York City coastal communities from a disaster such as Hurricane Sandy.

Directs the Administrator of the Environmental Protection Agency (EPA) to study the environmental impact of each major disaster that will have a significant environmental impact on U.S. waters.

Makes one of the goals of national freight policy to ensure that the socioeconomic and environmental impacts of moving cargo through a community are fully accounted for in establishing the national freight network (composed of highways, railways, navigable waterways, seaports, airports, freight intermodal connectors, and aerotropolis transportation systems most critical to the multimodal movement of freight).

Directs the Secretary of Transportation (DOT) to ensure that ports and harbors are incorporated into the national freight network.

Authorizes the Secretary of the Army to make grants to states and local governments for projects to improve port infrastructure and intermodal rail and highway networks.

Directs the Administrator of the Maritime Administration, acting jointly with the EPA Administrator, to establish a green port designation for ports that meet certain environmental standards.

Authorizes the Administrator of the Maritime Administration to provide grants and technical assistance to a designated green port to implement innovations that minimize the environmental impacts of port operations.

Directs the Secretary of Commerce, acting through the Administrator of the Economic Development Administration (EDA), to make grants to states and local governments for projects to establish environmentally sustainable waterfront areas. Sets the federal share of project costs at 75%.