The article, and most particularly its conclusion that all federal prisoners are unconstitutionally confined, is off the mark. Your son lacks a full understanding of Congress' powers under the Constitution, which lead him astray in his analysis.

 Congress does not need to fit all criminal laws under the Commerce clause for them to be valid under the Constitution. The Constitution expressly provides for a few crimes, like treason, and the bulk of the rest get their authority from the following provision of the Constitution giving to Congress the power, "To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution in the Government of the United States, or in any Department or Officer thereof." US Const. Art 1, §8, Clause 18 (the final clause of §8). Commonly known as the "necessary and proper clause" it is the foundation of much federal legislation, not just criminal laws. While this greatly oversimplifies it, so long as the Act passed by Congress can be tied to carrying out one of its enumerated powers, it is likely to pass muster under this clause. Thus, for example, the federal tax crimes set out in the Internal Revenue Code (IRC) are constitutionally valid because they are necessary and proper to enforce Congress' power to lay and collect taxes. The federal government could not effectively enforce the law laws without laws imposing sanctions for violators. The Cornell Law School has a nice overview of the necessary and proper clause, including a section on federal criminal law.