Cape Air is the main airline between BOS and ACK. JetBlue also has a few flights. Expect pricing similar to SXM-SBH prices - on the right day you can do OK, but on other days not so much.
Your choices to get from BOS to Hyannis are the bus, a car service, a rental car, or a train (Fri-Sun only) from South Station. The train option is relatively new, now in its second season, and only does 1 R/T per day.
http://capeflyer.com/
There's ample parking around the ferry terminal if you rent a car but can't arrange a pair of one-way rentals.
Flying to ACK and skipping the ferry is the best option.