Of the ones I've been to (all in the last decade) I would rank best to worst condition:
Fort Macon, NC
Fort Gaines, AL
Both very well-preserved and interpreted. Slight edge to Fort Macon because it's not altered by a later Endicott battery within the fort, although Gaines' is fairly small.
Fort Pulaski, GA
Could get the number one spot, depending on whether you think unrepaired damage from the 1862 bombardment is a benefit or a detraction.
Fort McAllister, GA
The best preserved and interpreted earthen fortification I've seen. I met a really nice reenactor last time I was here.
Fort Clinch, FL
Only small alterations. Before the pandemic they had weekend reenactors there monthly which adds a lot to the experience.
Fort Jackson, GA
Small and with a fairly minor role in the war, but in pretty good condition. The same historical society operates this fort that also operates the history museum and railroad museum in downtown Savannah so you can get an all-in-one pass.
Fort Moultrie, SC
Good condition and interpretation, but lots of alternations and additions from being used all the way through WW2.
Castillo de San Marcos (Fort Marion), FL
The NPS predominately interprets the fort's original and more significant role during Colonial Spanish Florida, but it was nominally still in use during the ACW.
Fort Barrancas, FL
The fort itself and the connected water battery converted from an older Spanish fort are in good shape, but it's small and not anything remarkable. The view has also been drastically altered by the construction of NAS Pensacola. However, you can spend a good day visiting Barrancas, Pensacola Lighthouse, and the Naval Aviation Museum all in very close proximity to each other.
Fort Sumter, SC
For all its historic significance, it's been heavily altered by the wartime destruction and postwar modifications. It's a level shorter than it was in 1861, 3 of the 5 walls are altered beyond recognition, and an Endicott battery dominates the site. It's a nice ferry ride across the harbor and still worth a visit for a history buff.
Fort Jefferson, FL
This one is a bit tricky to rate as it's an architectural marvel but also an architectural mistake. Not one of the ones in better condition, but it was never finished, the lower bricks are of inferior quality, the walls are filled with dredged coral, and the fort is simply too heavy for the island it's built on. It's a unique and fascinating experience. Worth the expensive day trip on the ferry from Key West.
Fort Fisher, NC
There's a good museum and one section of the massive earthwork, but of all the forts I've been to this one has the least to see.
Fort Pickens, FL
30 years ago Gulf Island National Seashore would have been great for coastal artillery buffs as you've got not only the main third-system fort, but a slew of later Endicott and post-Endicott fortifications too. As of a decade ago though the park was understaffed, underfunded, and not in very good condition. Lots of graffiti and most of the fortifications no longer open to the public. The main ACW fort is one of the more deteriorated I've seen. One of the bastions is gone due to a later magazine explosion. The view from the fort has also been substantially altered by Ivan and other hurricanes, there is an Endicott battery in the middle of it, and the mouth of Pensacola Bay has shifted substantially westward since the 1860s.
Fort Morgan, AL
One of my more recent visits and I was really surprised, especially in contrast to Fort Gaines across the bay (the ferry ride is worth it). It was not in very good condition and there was little interpretation. Endicott battery in the middle of it too.