Now that you're underway again...
We liked the Harborwalk Marina in Georgetown; didn't get a chance to stop there on our southbound route this time, but we found it to be a pleasant town on our previous trip... and we're hoping to stop there on our way back north eventually. The Rice Museum was informative (who knew?) so worth a visit. At least two very good restaurants in town on the water side, easy walk.
Charleston options include places like the Charleston Harbor Marina -- on Hog Island, not exactly Charleston at all, said to be expensive, but... just next door to the USS Yorktown facility, and that's very much worth a visit. More better for direct downtown access -- very pleasant town, well worth some time -- are the Charleston City Marina (aka Megadock) and just next door to that, the Harborage at Ashley Marina if they have space. The latter is a condo-type place, but we were able to stay there for a few months on our previous trip, decent. There are three free bus routes servicing the downtown peninsula, both City Marina and Ashley have shuttles, etc. It helps to arrive at slack water on the Ashley River, so Isle of Palms Marina could be a useful staging point to get your timing right. (Last trip, as we were steaming north past Isle of Palms on our way home... lo and behold, another TF member came out just then... so we had an impromptu "TF Get-Together" of sorts on the radio.
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Beaufort -- the one that's pronounced Beaufort -- seemed like a nice two-day town for us this year, our first visit. We stayed at the Downtown Marina at Beaufort (pronounced Beaufort) and it was OK, very central to the downtown area (as the name implies).
Even over several trips, I've yet to see downtown Savannah... and we hope to do that this time on our way back north. That said, I've stayed at Thunderbolt Marina a couple times over the years (remember the Krispy Kreme) and it's a decent marina with easy-enough access via Uber or whatever to downtown. And Tubby's is a decent restaurant, just up the street a couple blocks. Isle of Hope Marina has been recommended, but there was no room at the inn as we were passing by this time. Staying on the boat in downtown Savannah has been almost universally un-recommended (?) although I see some here have found it OK.
-Chris