Thanks for the suggestions. I like Frye boots a lot and have been wearing a Frye chelsea-style boot I've had for a long time on my bike, but was looking for something with more support and protection.
Chipppewa's a good suggestion too. In fact, after casting around the internet, I decided to go with that company, but a different boot, the 'Rally.'
http://www.chippewaboots.com/boots/rally/27862
The patch of leather for shifting gears shouldn't be too noticeable and it has a narrow, traditional shape. The velcro should be hidden under my cuff most of the time too.