Columbia Harbour House is our favorite for its location, accessibility and variety. Cosmic Ray's is often loud and overwhelming. It looks gigantic, but finding an open table at mealtimes is a hassle, and the food quality doesn't justify the stress. Even in the age of forums and chat rooms, where keeping a secret is practically impossible, Columbia Harbour House has gone overlooked. Sitting upstairs watching people milling around Liberty Square while eating lunch is a real pleasure.
Try the Lighthouse sandwich with hummus and broccoli slaw on a delicious thick multigrain bread. It's light and healthy, and a wonderful respite from all the fried junk you will certainly be eating the rest of the trip.
Pecos Bill receives fantastic reviews, but I have never enjoyed anything there.
Good luck!