According to the FEIS, government agencies worked together (and with the developer) to create design guidelines.
The Executive Summary states:
As part of the development of the proposed project, the project sponsors worked closely with City Planning and ESDC staff to develop Design Guidelines that establish a framework for the design of the project. The purpose of this effort and the Design Guidelines was to identify the important elements of the project master plan developed by Gehry Partners and Olin Partnership and require that these elements be incorporated into the project, while at the same time providing enough flexibility to allow for the final design of the individual buildings to evolve as the project is built out.
Chapter 1 (Project Description) of the FEIS is a bit more obfuscatory:
In order to establish an overall framework for the design and development of the project site, the proposed project would follow urban design goals and principals set forth in a set of Design Guidelines developed in close consultation with ESDC [Empire State Development Corporation] and DCP [Department of City Planning} staff. The Design Guidelines are attached as an exhibit to the GPP. The Design Guidelines were supported by the New York City Planning Commission (CPC) in its recommendations on the project and have been modified since issuance of the DEIS to reflect CPC’s recommendations.
It came from Gehry
The agencies did contribute to the Design Guidelines. Memos acquired via a Freedom of Information Law request to DCP show that DCP staff commented to representatives of developer Forest City Ratner, architect Frank Gehry, and landscape architect Laurie Olin.
However, the job to "identify the important elements of the project master plan developed by Gehry Partners and Olin Partnership" seems to have been mainly the responsibility of... Gehry Partners. As the memo reproduced here shows, Gehry took the lead, and the agencies agreed with Forest City Ratner's plan to take Gehry's name off the guidelines.
Note that the original Memorandum of Underestanding, from 2/18/05, was ambiguous, stating that the Public Parties would work with the developer.