Greetings. I am a local. I keep my boat across the river from North Philadelphia, and have made the trip to and from the bay more than fourty times.
Philadelphia as a destination - there is a great deal to do in Philadelphia, people travel from all over the world (and particularly the US) to visit it. A tremendous amount of history, several great museums (Phila Art Museum, Franklin Institute, Rodin Sculpture, etc. , Old town / Liberty Bell, many great restaurants, concerts classical and pop, funky street life (South street on a Saturday night), night clubs (some on the waterfront), etc. Check TripAdvisor or any travel resource.
Marinas - unfortunately the options have gotten worse in the last couple years.
The web sites on the internet look to be mostly out of date........
Philadelphia Marine Center is closed permanently (for a year now) for redevelopment. Have not heard future plans yet.
Slips next to Dave and Buster's restaurant are silted in with mud and not usable for several years now.
Penns Landing is still a functioning marina, but most of their slips are now permanent season tenants, I understand they maintain three or four transient slips (call them for reservation). Be advised there are no restroom facilities (except public restroom across the way in the park (yuck). Be prepared to head/shower on your boat. Facility is safe, the promenade is locked at night with access only to marina guests. Nice onsite manager in the summer time. Great location, great access to the city.
Pier 5 (actually pier 3 & 5) marina - this small marina is between the blue waterfront pier/condo's pier 3, 4 and 5. It is run by the Delaware Waterfront Corporation. Most slips are for annual season but they have a few transient slips (call to check reservation). This is NOT a luxury marina, though you would think it is; temper your expectations. There was a small head at pier 5 last time I went. The location however, cannot be beat, you are right on Delaware Ave with access to taxi/Uber/Lyft and subway is a few blocks away. Staff may or may not be onsite, but are available by phone.
Travel to/from Phila. The key is to be aware of the tidal current. Stage yourself at Delaware City for the night. Go to Crabby Dick's restaurant for a fun/funky meal. Nice management at Delaware City Marina (highly recommended). Clean (if small) shore heads, locked gates in the evening, diesel/gas available, nice small marine store and gift shop. This is a key stopover for the Great Loop travelers.
Time your trip up the river and back with the current, it is the difference between 8 kts (6 hours), and 4.5 kts (10 hours). Yes, it is 95% motoring and a commercial/industrial waterway. No marina options along the way except at Tinnicum (just below Phila airport) behind the barrier island - by then you are almost at Philadelphia.
The path is very clearly marked (buoyed), and wide. Ocean going ships transit all the time, and plenty of room for you to stay out of the way. Just watch your chart plotter for the shallows. Yes there is one submerged bulkhead just above Del City, it is well out of the way and not an issue.
After a heavy rain, watch for logs/wood in the water.
Given that you have a reservation at one of the options above, enjoy the city. It has much to offer any age.
Just power through the industrial river. No different than in/out the Patapsco, just longer.
Hope that helps.