This is an old thread but my advice may help someone other than the OP.
Hard question. I'd buy three bikes, one from each.
Agees has been in business for over a hundred years and is still run as a friendly family-owned business carrying good bikes & accessories and giving good service. I've bought 8 bikes from Agees over the years.
Conte's expanded to this area from tidewater Va. and came with high quality bikes, quality service and enough patience to deal with customers who are still learning. They special-ordered some parts for one of my vintage bikes when some shops would have just said so-sorry. They recently moved to a new location in Short Pump.
Carytown Bikes is a quality bike shop run by what appear to be urban riders in their late-20's. They offer great bikes and friendly service. They have an open repair area so you can see what's being done. They are never too busy to help, and they even do a lot for the community such as offering free use of tools and a place to do your own work on your bike if you prefer. They are convemient to the Fan and downtown, right in Carytown on Cary St.
In addition to those mentioned, I like 3-Sport; the mechanics are fantastic. I also like Bunny Hop in Oregon Hill. There's a newish shop on Broad near VCU called Balance Bicycle Shop that looks pretty neat from the outside (urban/commuter bikes in window) but I haven't been there yet.