M2, I went to both on a cruise several years back and both islands had been devastated by a recent hurricane. Kitt is much smaller and quiet, if you stay away from the port. (Cruise people arrive as a mob). Thomas has much more in terms of duty free items, but that doesn't sound like what you are looking for.
I think if you find the lodging that meets your needs, either island will suit you. I'm curious...why these two islands?