I think your parents would like the Smith Cove Inn. With proper booking you can guarantee a slip for their boat. They have several lovely rooms and a nice breakfast to kick off the day. We stayed there several time before we got our place on Cow. We have also had friends stay there.
Would they be able to launch the boat each day? If so Lakeport Landing has a nice boat ramp and you can usually get a place to park on the street. Then simply tow the boat to the Margate or Churches Landing, et al. It certainly is more economical.
We stayed at Center Harbor once but the rooms were so so and the mattress was lumpy.Not sure what they have done to improve the place. I think we stayed there around 2000.