Don't you ever look anything up? Guess not -- I know better than to ask. Here apparently is what he was arrested for.
Case of Henry A. Reeves.
This person was arrested by order of the Secretary of State about the 2nd of September, 1861, at Greenport, Long Island, and committed to Fort Lafayette. He was the editor of a paper published at Greenport called the Republican Watchman, which by its secession teachings and attacks upon the acts of the officers of the United States Government and the Administration afforded aid and comfort to the insurrectionists.
Attacks on the acts of officers of the US government? Where was John McCain and CFR when Lincoln needed them? You can't criticize the government or its officers! < / sarc>
Aid and comfort to the enemy? That's one of the definitions of treason, isn't it? First amendment doesn't protect against criminal acts.