Henry Halleck, George Ripley was detrimental in some ways, General ___ Twiggs was a detriment early on with Texas, General Nathaniel Banks was a BIG detriment in 1864, I would say Clement Vallandigham was a detriment, but he was more of a distracting annoyance than anything. Also I think Fernando Wood was something more akin to an annoyance than a big problem for the War effort.
Here's one that'll cause controversy, and to me the biggest detriment, till he mostly got out of the way, Abe Lincoln.
Before anyone loses their mind, just here me out, and think about it, his constant meddling in the military's affairs probably did more harm than good, demanding an Army to move on the Confederacy before they were ready too, he would appoint political buddy's of his to senior generalships when they had no experience, he'd appoint political enemies to high up generalships to get them out of his way and they'd muck up everything as bad as his buddy's with general stars, he'd persuade the military to buy from companies he had connections too when they could be acquired elsewhere at better prices, he'd fire generals who may have decent otherwise after he placed them in an impossible positions they weren't good for, (Burnside had some merits, and knew he wasn't qualified for the senior command, Lincoln promoted him anyway), Lincoln would put political agendas ahead of military ones and the military would suffer as a result, and the list could on.
I think Lincoln redeemed himself to some extent after he promoted Grant and stayed the h**l out of the way, but the Union may have had a better chance of winning the War as early as 1862 if he had stayed out of the way. Hence why I consider Lincoln the biggest detriment to the Union war effort, he may have meant well, but he botched it royally time and again when he exercised his authority over the Army.