He served as Director for Global Affairs on the United States National Security Council from 1995 to 1997, where he coordinated policy for the prevention of drug and migrant smuggling.
In 2009, Boynton was nominated by former Governor M. Jodi Rell to be the state of Connecticut's next Commissioner of the Department of Emergency Management and Homeland Security (DEMHS).
[5] Of the nomination, Governor Rell said: "Peter's decades of dedicated service to our nation, the many roles he has played in the Coast Guard and his experience at Bradley combine to make him an ideal candidate for the many tasks that befall the Commissioner of the Department of Emergency Management and Homeland Security.
From planning and drilling for natural disasters and potential terrorist attacks to working with me to respond to major storms to collaborating with our Congressional delegation and local leaders on issues of homeland security funding, DEMHS is essential to what I have often described as government's foremost responsibility: ensuring the safety of its citizens.
During his tenure, Boynton testified before the U.S. Senate Committee on Homeland Security and Governmental Affairs regarding ongoing planning to prepare for a possible Fall 2009 H1N1 outbreak in the State of Connecticut.