Rick doesn't list too many restaurants with roof top views like that but here are two that he does mention. Having personally been to the Strofi restaurant, the food was great and the view from the terrace was worth it. I hope this helps some.
Strofi Athenian Restaurant is my favorite place in town for white-tablecloth, elegantly modern, rooftop-Acropolis-view dining. A five-minute walk from the tourist crush, Niko Bletsos and his staff need to be as good as they are. Once you’re seated on their rooftop enjoying classic Greek cuisine--especially lamb--under a floodlit Acropolis, you’ll be glad you made dinner reservations here. And though they have a fine air-conditioned interior, the breeze makes the rooftop comfortable even on hot evenings (€6-10 starters, €13-17 main dishes, Tue-Sun 12:00-late, closed Mon, about 100 yards down Propyleon street off Dionysiou Areopagitou at Rovertou Galli 25, tel. 210-921-4130, www.strofi.gr).
Splurge: Hotel Grande Bretagne’s Roof Garden Restaurant is considered by many the finest place in town to dine on Greek and Mediterranean cuisine in pure elegance--in a rooftop garden with spectacular Acropolis and city views (€20-25 pastas, €25-45 main dishes, plan on spending €60 for dinner, daily 13:00-1:15 in the morning, reservations required for meals, “smart casual” dress code, north side of Syntagma Square, tel. 210-333-0766, www.grandebretagne.gr). If you don’t want such an expensive meal, drop by their bar for a €10 beer or a €16 cocktail.