I'm making a general post since some folks may be interested. I hardly ever read my email on this account and there was an old one in there from last month inquiring about cheap rooms for Tradewinds. Here's a very short list of places I know of around here. And remember to haggle any place. Despite what they may tell you it is NOT high season here during Tradewinds.
I haven't researched their room rates, but these are local mom and pop places you might not know about:

Key Lantern
Drop Anchor
Harbor Lights
Tavernier Inn

If any other locals know of some little spots please post in this thread.