I agree with Hawker800. The Nantucket Inn is ok for a quick overnight. But if you're visiting the Gray Lady for more than 1 night and $$$ is not an overwhelming concern, definitely stay in town. The Roberts House (if you can get in) is an excellent B&B, centrally located at the corner of Center and India Sts. They have a great porch that lends itself to hangin' out with friends and sharing a bottle a vino. 76 Main Street Inn is also a pilot friendly place to hang, and right in town.
A couple other suggestions: You don't need (or want) a rental car. You can cab into town, then walk / bike everywhere else. Assuming you'll be there more than one night, rent bikes and ride the island. Ride out to the Wauwinet for an awesome lunch. The Atlantic Cafe in town has a great menu and awesome chowder.
Sorry if I sound like a Chamber of Commerce ad for ACK. I've spent quite a bit of time there and it's one of my favorite destinations.
Side note: There's a TSA agent that likes to show up at the GA gate, at odd hours, in civvies looking like she's lost. She's watching the gate and looking to see if crews get properly ID'd. Don't open the walk through gate for just anyone. Be sure to have the folks in the FBO look at your ID's as you walk through.
Enjoy!