You do know that the Constitution specifically allows for suspension of habeas, and that congress subsequently confirmed Lincoln's actions, right?
Article I, Section 9:
The Privilege of the Writ of Habeas Corpus shall not be suspended, unless when in Cases of Rebellion or Invasion the public Safety may require it.
Was Maryland in Rebellion or being Invaded May 25, 1861?
Yes, of course, but as Hamilton and Jay said above, habeas corpus may not be suspended except by Congress. Many other founders, ratifiers, the Supreme Court, a previous president, etc., held the same view, as you no doubt know.
Congress does not have the authority after the fact to approve an unconstitutional action of a president. They indemnified Lincoln for his actions, but what he did was unconstitutional. A couple of years after Chief Justice Taney's valid legal order (Ex Parte Merryman) against Lincoln's suspension of habeas corpus (which Lincoln ignored), Congress authorized Lincoln to suspend habeas corpus in the last years of the war. If Lincoln had the constitutional power to suspend habeas corpus, why did Congress indemnify his 1861 actions and later authorize him to suspend habeas corpus for those last years.
As the Supreme Court later said in Ex Parte Milligan in a unanimous decision delivered by Lincoln's good friend (and executor of his estate, I believe), Justice Davis:
The Constitution of the United States is a law for rulers and people, equally in war and in peace, and covers with the shield of its protection all classes of men, at all times and under all circumstances. No doctrine involving more pernicious consequences was ever invented by the wit of man than that any of its provisions can be suspended during any of the great exigencies of government." (Justice Davis, ex parte Milligan, 71 U.S. 2, (1866))
From Taney's Ex Parte Merryman order:
The constitution provides, as I have before said, that 'no person shall be deprived of life, liberty or property, without due process of law.' It declares that 'the right of the people to be secure in their persons, houses, papers and effects, against unreasonable searches and seizures, shall not be violated; and no warrant shall issue, but upon probable cause, supported by oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.' It provides that the party accused shall be entitled to a speedy trial in a court of justice.
These great and fundamental laws, which congress itself could not suspend, have been disregarded and suspended, like the writ of habeas corpus, by a military order, supported by force of arms. Such is the case now before me, and I can only say that if the authority which the constitution has confided to the judiciary department and judicial officers, may thus, upon any pretext or under any circumstances, be usurped by the military power, at its discretion, the people of the United States are no longer living under a government of laws, but every citizen holds life, liberty and property at the will and pleasure of the army officer in whose military district he may happen to be found.