If you are considering Manchester, look into some of the park-n-fly rates at the local hotels. We've found that it's usually more affordable to park at a hotel the night before our flight and pay to leave the car there for the duration of the trip. I believe Concord Coach runs a bus from MHT to BOS (but it could be CandJ bus).
Second suggestion: I am not sure how long the drive to Portsmouth, NH, would be, but if you are flying out of Logan, consider driving to Portsmouth and parking at the CandJ Bus parking lot and taking the bus into town. Parking is free, and the bus runs pretty much hourly. I also think (could be wrong) that if you call them when the bus leaves Logan on the way home, they'll bring your car from the lot right to the terminal (but you might have to valet park for this, I'm not sure).
Just make sure that you'll be saving enough in airfare to be worth the hassle of getting to Logan.