...Is the concern debris in the water? Would the marinas be protected against this - it seems that Phila Marine and Piers are both quite protected. Maybe higher winds tipping the boat?
I spoke to Chuck at The Piers Marina yesterday about getting a transient slip this weekend, and he said that there is severe shoaling in the marina right now, and expected to stay that way until they dredge. You should keep this in mind, and don't sign a contract until you've confirmed that their dredging is compete and successful. He said they have their permits and should dredge this fall/winter. But do your due diligence, because these things have a way of being delayed for months or years.
The configuration of both of these marinas (surrounded on three sides) makes them very protected from currents. Debris will find its way in gradually and stay there forever until somone hauls it out. Silt will deposit gradually until they dredge, and then will start to deposit again. It's not a deal killer, but you need to be sure they stay on top of it.
The Piers is surrounded by buildings on three sides. This could protect pretty well from winds and gusty storms, but could also make it really bake in the summer. But I'm not speaking from any personal experience with these particular marinas, so try to get local knowledge from someone. When I was looking for marinas I hung around and walked the docks talking to people.
For this weekend we decided to try out the newly renovated Penns Landing marina. The bathrooms and showers are more remotely located there (if they exist at all - but Monica said they have them), but this isn't a big issue for a one night stopover. Looking at the satellite pic, it looks like a pretty neat setting to take a slip along the seawall only 100 feet from Moshulu, with River to the east and skyline to the west:
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