Have a look at Neal Stephenson's Baroque Cycle (Quicksilver, The Confusion and The System of the World). Stephenson's best known for his science-fiction, but this is proper historical fiction.
It's set against a background that includes the establishment of the Royal Society (and a pirate story), and features both romance and a strong female character. It's a lot better than I've made it sound, and I recommend it highly.
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