Securing Maritime Activities through Risk-based Targeting for Port Security Act or the SMART Port Security Act – Title I: Department of Homeland Security Port Security Programs – (Sec. 101) Directs the Secretary of Homeland Security (DHS): (1) by July 1, 2014, to submit a plan for the coordination and cooperation of maritime operations undertaken by DHS agencies that updates the plan released by DHS in July 2011; and (2) by July 1, 2019, acting through DHS’s Office of Operations Coordination and Planning, to submit an additional update to such plan. (Sec. 102) Requires any new asset deployment by the U.S. Customs and Border Protection’s (CBP’s) Office of Air and Marine to occur in accordance with a risk-based assessment that considers mission needs, performance results, threats, costs, and other specified factors. (Sec. 103) Directs the Secretary to conduct a cost-benefit analysis to consider potential savings derived from co-locating aviation and maritime operational assets of Office locations that are within 25 miles of locations where any other DHS agency also operates such assets. (Sec. 104) Directs the Comptroller General to: (1) review port security and maritime law enforcement operations within DHS to identify initiatives and programs with duplicative, overlapping, or redundant goals and activities and recommend actions to reduce unnecessary duplication; and (2) submit a report that analyzes and compares the costs, capabilities, and missions of different aviation assets utilized by DHS to assess the relative costs and any benefits of unmanned aerial vehicles compared to manned aviation assets. (Sec. 105) Directs the Secretary to: (1) coordinate across DHS agencies before initiating the acquisition of any new boat or aviation asset; (2) establish a coordinating mechanism for aviation and maritime issues in order to decrease procurement and operational costs and increase efficiencies; (3) approve or disapprove a complete application under the Port Security Grant Program within 60 days of submission; (4) submit an assessment of interagency operational centers for port security, the deployment of interoperable communications equipment to such centers, and center mission execution and support activities; (5) submit a report analyzing the threat of, vulnerability to, and consequence of a terrorist act using a small vessel to attack U.S. vessels, ports, or maritime interests; and (6) submit a plan for optimizing CBP staffing levels. (Sec. 112) Amends the Homeland Security Act of 2002 to authorize the Secretary to establish an Integrated Cross-Border Maritime Operations Program to coordinate maritime security operations between the United States and Canada. Directs the Commandant of the Coast Guard to administer the Program in a manner that results in a cooperative approach between the United States and Canada to strengthen border security and to detect, prevent, suppress, investigate, and respond to terrorism and violations of law related to border security. Authorizes the Commandant to: (1) establish, as an element of the Program, a training program to create designated maritime law enforcement officers; and (2) conduct training jointly with Canada, including training on the detection and apprehension of suspected terrorists and individuals attempting to unlawfully cross the U.S.-Canada border and on the integration, analysis, and dissemination of port security information between the United States and Canada. Authorizes appropriations for FY2013-FY2014. (Sec. 113) Authorizes the use of port security grant funds to cover the cost of certifying a law enforcement officer employed to enforce security zones for the transportation of especially hazardous cargo. Directs the Commandant to establish standards for training, qualification, and certification of a law enforcement officer employed by a law enforcement agency to conduct or execute maritime security, maritime law enforcement, and maritime surge capacity activities pursuant to a cooperative enforcement agreement. Authorizes the Commandant to: (1) issue a certificate to a law enforcement officer who has successfully completed training that the Commandant developed; and (2) make such training available a to officers of a law enforcement agency if a Coast Guard member is unable or unavailable to undertake tactical training previously approved, no other Coast Guard member is reasonable available to undertake such training, such inability or unavailability creates capacity within the training program, and making such training available to such law enforcement officers would contribute to achievement of the purposes of providing such training. (Sec. 114) Directs the Secretary to: (1) research and develop technologies to allow routine operation of medium-sized unmanned aerial vehicles, including autonomously piloted drones, within the national airspace for border and maritime security missions without any degradation of existing levels of security-related surveillance or of safety for all national airspace system users; and (2) commence a pilot project in segregated airspace along the northern border to conduct experiments and collect data in order to accelerate the safe integration of medium-sized unmanned aircraft systems into the national airspace system. (Sec. 115) Authorizes the Secretary to: (1) treat a foreign port security assessment conducted by a foreign government or international organization as an assessment by the Secretary if the Secretary certifies that it was conducted in accordance with existing security effectiveness requirements; and (2) enter into an agreement or arrangement under which a foreign government or international organization may conduct a required assessment of the antiterrorism measures at a foreign port on behalf of the Secretary, or share with the Secretary information pertaining to such assessments, or under which the Secretary may conduct such an assessment on behalf of such government or organization, or share with such government or organization information pertaining to such assessments. (Sec. 116) Includes replacement costs of security equipment or facilities among eligible costs for funding under port security grants. Title II: Maritime Supply Chain Security – (Sec. 201) Amends the SAFE Port Act to: (1) revise requirements for the strategic plan to enhance the security of the international supply chain, including to add requirements to identify redundancies or overlaps in federal transportation security credentialing programs and to make recommendations for facilitating the efficient flow of legitimate commerce; and (2) require the Secretary to submit an additional update to, and an implementation plan for, such strategic plan and to consider current threats to the global supply chain. (Sec. 202) Authorizes the CBP Commissioner to conduct an unannounced inspection of a Customs-Trade Partnership Against Terrorism (C-TPAT) participant’s security measures and practices upon determining, based on previously identified deficiencies, that there is a likelihood that such an inspection would assist in confirming the security measures in place and further the validation process. Directs the Secretary to promote information sharing among DHS and C-TPAT participants and other private entities regarding: (1) potential vulnerabilities, attacks, and exploitations of the international supply chain; and (2) means and methods of preventing, responding to, and mitigating consequences from such vulnerabilities, attacks, and exploitations. (Sec. 203) Directs the Secretary, before negotiating or signing any arrangement between the United States and a foreign government providing for mutual recognition of supply chain security practices, to determine and notify Congress that the foreign government’s program provides comparable security to that provided by C-TPAT. (Sec. 204) Requires the Secretary to develop a pilot program to determine whether allowing non-asset based third party logistics providers that arrange international transportation of freight to participate in C-TPAT would enhance port security, combat terrorism, prevent supply chain security breaches, or meet C-TPAT goals. Requires: (1) participation by such providers to be voluntary, (2) the Secretary to ensure that not fewer than five such providers take part in the pilot program, (3) the pilot program to be conducted for at least a year, and (4) the Secretary to report on the findings and any recommendations concerning the participation of such providers in C-TPAT to combat terrorism and prevent supply chain security breaches. (Sec. 205) Expresses the sense of Congress that it is urgent that the Transportation Worker Identification Credential (TWIC) application process be reformed by not later than the end of 2012. Directs the Secretary to reform the process for the enrollment, activation, issuance, and renewal of a TWIC to require not more than one in-person visit to a designated enrollment center, except under extenuating circumstances. (Sec. 206) Provides that a valid TWIC that was issued before the date of this Act’s enactment shall not expire before the earlier of: (1) the deadline for full implementation of a final rule for electronic readers designed to work with TWICs as an access control and security measure, or (2) June 30, 2014. (Sec. 207) Directs the Secretary to establish a process to ensure that an individual who is not lawfully present in the United States cannot obtain or continue to use a TWIC. (Sec. 208) Directs the Secretary to submit to the appropriate congressional committees a report that identifies unnecessary redundancies or overlaps in federal transportation security credentialing programs and recommendations to reduce or eliminate such redundancies or overlaps.