Just inside the Inlet you have North Marina that has nice dockage. The indian River & Rehobeth Bays are very shallow even at High tide you must follow the markers or you will be in trouble. IMO there is not much room to run in those bays although there is a cool bar/restuarant called the Rusty Rutter tthat you can dock your boat at for a few beverages.
My parents have a place on the Rehobeth Bay and when I visit I usually do not take my boat (Donzi 22 classic) because of limited running. If you have a bigger boat you have all kinds of running in the ocean which is NICE!!!