This thread began as a Cedar Point discussion, but contains a lot of useful info about PIB as well:
http://clubsearay.com/forum/showthread.php?t=27148&highlight=crew%27s+nest
As stated, The Crew's Nest is members-only on wkds, but accepts transients Sun-Thurs. (with some exceptions) TCN holds the largest number of private docks and boasts the best amenities, including: a large outdoor pool, play area, snack bar, a fitness ctr, racquetball court, tennis courts, sauna, hot tub, lap pool, clean restrooms, patio restaurant, bar, formal dining, gift shop, cart rental etc.
Miller's Marina is also a good option. They accept reservations. Millers has very clean restrooms (limited tho) and a nice pavilion / picnic area. They will only allow rafting at the request/permission of the boaters. (if traveling in a group etc) Miller's is far enough from town to be quiet, if that's what you're looking for. They recently added a small rental fleet of golf carts (the preferred method of transportation on the island).
Ladd's Marina, now called "Put-In Bay Marina" has a great location - the closest to the monument and most of their wells are protected from open water. Their basin has some skinny / weedy areas, and the docks have seen better days, but the proximity to town and the new dockside grill/bar and nice restaurant make it a worth a look.