There aren’t many truly unique pickups. There’s only so much you can accomplish by reconfiguring the machinery/electronics involved. That being said, I personally would suggest looking into “Jazzmaster pickups” (named due to being the pickups from the Fender Jazzmaster guitar) as one of the truly distinctive single coil options (they’re particularly effective at “darker” clean tones, as opposed to the brighter jangling characteristic of something like the Stratocaster).
You might not be able to accomplish installation without some professional assistance though, I’m not sure. At the very least you would need some sort of new pickguard for your Stratocaster to accommodate the shape/size.
Here are some video examples of Jazzmaster pickups installed on a Strat. (I don’t know how good these videos are, or if the players do a good job of representing the sound you can expect. I haven’t watched them. But it’s the only two videos I could find on YouTube of this)