This is going to sound horrible (sorry), but (in my opinion), the Warehouse, Geranios, and Indigo Landing are all overpriced tourist traps and mediocre (at best). The Chart House is a corporate chain restaurant and is similarly mediocre and expensive. I've lived in Old Town for many years and (unfortunately) have eaten at all these places many times (always hoping that they get better, but they never do).
Old Town has some great restaurants, however. Some of my personal favorites (to respond to your request for "best'):
1. Restaurant Eve's Tasting Room is the best restaurant in Alexandria, but comes with splurge/anniversary/birthday pricing. Eve (non Tasting Room) is not as recommended because I think the value for money is just not there.
2. The Majestic. "Homemade" and simple food with a touch of elegance. I think they only thing they don't make is the Amish butter. They make fantastic mixed-drinks at the bar.
3. Le Refuge - throwback country French place on Washington. This place is a time warp of a 70's/80's French restaurants with all the kitchy Nouveau Beaujolais posters and wine bottles. The food is quite good, however.
4. Society Fair Demo Kitchen. If you want to do something quite fun/different, sign up for the Demo Kitchen at Society Fair. This is a new restaurant/food emporium in Old Town with a different food theme every night. You sit at a bar and the chef does a cooking demonstration for 6-8 people while you watch and eat.
5. Hank's Oyster Bar - more than just oysters. Lobster roll! They also have red meat options.
6. Brabo - can be expensive. Nice wine list.
Some casual places:
1. Momo sushi (on Queen);
2. Caphe Banh Mi (Vietnamese on Cameron)
3. Eammon's (fish and chips on King)
4. Le Pain Quotidien (for breakfast - on the corner of King and Washington)
5. BGR (great burgers, shakes, fries and onion rings on Washington)
6. Pizzeria Paradiso (pizza and great beer list on King)
Really the only other place with a river view is Mai Thai, which has reasonable Thai food (although Virtue may have a peek - Virtue has been a bit of a miss, for me, however and I can't recommend it).
Edited: 11:11 am, August 28, 2012