Yes, Lincoln visited here. He came to New York to deliver his Cooper Union speech except, as I mentioned in a previous post, he was originally invited to speak in Henry Ward Beecher's Plymouth Church in Brooklyn. Above is a picture of the pew where he sat on February 26, 1860. He delivered his speech at Cooper Union and returned to sit and worship in the balcony two weeks later.
The church itself has an interesting history. Built in 1849 in Brooklyn Heights, it seated over 2,000 people. Its chief preacher was Henry Ward Beecher, depicted in a statue above. Though not an abolitionist, he was anti-slavery. He held fourteen slave auctions in which money was raised to free bondsmen in the South. The church was also a way station on the Underground Railroad. From here, church members ferried slaves up to New England by ship or overland. It is speculated that slaves were hidden in the church basement. In addition, church members concealed slaves in storerooms inside their own homes.
As mentioned before, though Brooklyn was not yet officially a part of New York City, the two cities were closely linked economically. New York was pro-slavery due to its close ties with the South. The city shipped goods southward and held the mortgages and loans made to many Southerners. Hence, being anti-slavery in Brooklyn in the years prior to war was anything but popular. The churchgoers also defied the Fugitive Slave Law in hiding and transporting bondsmen.
Henry Ward Beecher's Plymouth Church can be visited by a quick hop on the subway across the East River into Brooklyn.