Back Bay Bikes is my personal choice (and I live near Ace Wheelworks). To me, it's all about the relationship you build with the employees. I find the folks at BBB to be very helpful. It's a small shop, but I've never needed something they don't carry or can't order.

I've been to Landry's on Comm Ave a few times. They're good, bigger than Back Bay.

I avoid Cambridge Bikes at all costs.