Captain Bryant has a great post on three recent Coast Guard Port Security Advisories related to defending U.S. flagged, commercial vessels from the threat of piracy.  The three advisories are available for download at his blog.

From the Coast Guard's advisory:

Working with our interagency partners we have identified at least three options under which firearms could be exported and used aboard vessels in compliance with the ITAR, 1) obtaining a temporary export license (DSP-73), 2) temporarily exporting firearms and ammunition under an exemption to the ITAR, and 3) purchasing foreign firearms and filing for a temporary import license (DSP-61) when entering U.S. ports. The option that provides the most flexibility for an owner or operator of a vessel would be to obtain a DSP-73 temporary export license in accordance with 22 CFR 123.5. (Please note that in order to apply for a DSP-73, you must first register with the Department of State. Information on registering is available below.) This license is valid for up to four years, may be used for multiple entries and exits, and would require the operator to identify and list on the license application the firearms or other defense articles (e.g., ammunition) to be carried aboard the vessel. Once the license is obtained the operator could then stow the firearms on board the vessel in a U.S. port and keep them stored aboard the vessel until needed for use within the High Risk Waters by the crew or contracted security teams. Prior to entering or exiting the United States the license holder or their authorized freight forwarder would present the DSP-73 to CBP officials as part of clearing customs. Prior to leaving the United States the license holder or their authorized freight forwarder would have to submit the Electronic Export Information (EEI) through the Automated Export System.

To be sure, this only applies to U.S. vessels carrying firearms when departing U.S. ports and there is a personal exemption detailed in the post.