I was born in Havre de Grace and grew up in Harford County. Some of my earliest memories are of catching "rock" (Striped Bass), crabs and body booting for geese and ducks in the Bay and on the Susquehanna flats. September is prime time for crabs, as they have migrated to the upper Bay by then. The water is still warm. Hurricanes are rare here but they can occur. Frankly, as far as I am concerned September is probably the nicest time to be there, smaller crowds, restaurants and marinas open but not crowded, etc.
All of the suggestions are good, and there are many places you can stay on the hook for free. Beware of Aberdeen Proving Ground in the north Bay, as there are restrictions. If you want to stay in north Bay, Rock Hall and Eastern Neck are great. You can buy a net and use a string and chicken neck to catch enough crabs to enjoy them. Bush River is excellent for crabs, as is the Elk River and Chester. Eastern Neck Wildlife Refuge offers a lot of shallow water where you can wade and scoop crabs up, and lots of tidal areas with grass where you can find softshell crabs. A softshell sandwich is quite a treat.
If you moor near Eastern Neck, look for a very large squirrel, about twice as big as a regular one. This is a "Delmarva Peninsula Fox Squirrel".
Further south you have lots of interesting places. For nature and birds Blackwater National Wildlife Refuge is unbelievable with the concentration of birds in September, though I have paddled mostly in a kayak as it is thick with vegetation as well. You might check with the park people about a C-Dory. You could certainly head up the Nanticoke River at least as far as Vienna and see much the same.
Going through the Chesapeake and Delaware Canal is fun, but watch for large boats as it is relatively narrow and busy. Shaeffer's Canal House near the entrance just up from the Elk River is a popular place and you can actually get seats in September, mooring your boat just outside. My guess is that you can go way up Delaware Bay, but you should visit Lewes Delaware, and Cape Henlopen Park if you like fishing and nature. Take a "head boat" at Lewes, Delaware, and eat at the restaurant near the marina. You can moor you boat at the city dock.
You can get into Rehobeth Bay by the Waterway. Again, phenomenal birds in September as many are migrating through. Cape May in New Jersey should have millions of migrating birds by then that crossing from Cape May to Cape Henlopen on their way further south. Millions of Canada and Snow Geese will fill the water and the air.
And you can catch a few crabs with a string tied to a chicken neck and a small net just about anywhere. I traded the Chesapeake for Puget Sound 30 years ago, also trading blue crabs for Dungeness crabs, but I expect "Problemadela" will make it out there in the near future.