The United States population in 1860 ----- 31,443,321
New York population in 1860 -------------------1,174,779
Jews made up 5% of America in 1860 ---- 1,500,000 but it's doubtful that 2,000 Jews served in the civil war. Jews settled in all the major trading centers along the Atlantic coast and the Mississippi.
I imagine that on the northern march on the south that zero synagogues were torched.