If one were simply to consider specific acts which constituted grave assaults on civil liberties - narrowly defined as the core political rights explicitly protected by the Bill of Rights: free speech, freedom from deprivation of life and liberty without due process, etc. - one could make a strong argument for several presidents. John Adams signed The Alien and Sedition Acts, which essentially criminalized certain forms of government criticism in preparation for a war with France, a radical assault on the First Amendment.
Abraham Lincoln illegally suspended the core liberty of habeas corpus without Congressional approval. Wilson's attacks on basic free speech in the name of national security were indeed legion and probably unparalleled. Franklin Roosevelt oversaw the due-process-free internment of more than 100,000 law-abiding Japanese-Americans into concentration camps.
And then there are the two War on Terror presidents. George Bush seized on the 9/11 attack to usher in radical new surveillance and detention powers in the PATRIOT ACT, spied for years on the communications of US citizens without the warrants required by law, and claimed the power to indefinitely imprison even US citizens without charges in military brigs.
His successor, Barack Obama, went further by claiming the power not merely to detain citizens without judicial review but to assassinate them (about which the New York Times said: "It is extremely rare, if not unprecedented, for an American to be approved for targeted killing"). He has waged an unprecedented war on whistleblowers, dusting off Wilson's Espionage Act of 1917 to prosecute more then double the number of whistleblowers than all prior presidents combined. And he has draped his actions with at least as much secrecy, if not more so, than any president in US history.
Ultimately, it is close to impossible to rank these abuses strictly as a qualitative matter, in terms of the powers seized. How does one say that interning citizens in concentration camps (Roosevelt) is better or worse than imprisoning people for dissent (Adams and Wilson), putting people in cages with no charges (Lincoln, Bush, Obama), or claiming the power to execute citizens in total secrecy and without any checks of any kind (Obama)? If anything, one could reasonably argue that the power of due-process-free executions is the most menacing since it's the only act that is permanent and irreversible.
