we will be arriving late on a sunday night (10pm) and picking up a rental car on monday morning at the airport. need a reasonable hotel with a shuttle service from the airport

Try Priceline for 4* in Logan zone. You'll get either the Hilton or the Hyatt Harborside.

jiker:

We enjoyed one night at The Embassy Suites last summer. Shuttle service was prompt picking us up at the airport and dropped us off at our car rental the next morning. Hotel serves a good breakfast as part of the cost. Customer service was excellent.

Sandy

I got the Hilton for $79 on Priceline in October. Walked to the hotel from Continental Airlines without ever leaving the airport, which was wonderful at 11:30 pm and having flown in from Tokyo!

We stayed at the Harborside Inn. Not luxury but small hotel right across the street from Quincy Market.

You can do this in reverse.

To get to the airport we took the elevator right outside the hotel down to the subway level. The subway dropped us off at the free shuttle to each terminal.

I imagine you can do it in reverse.

Why not pick up the rental there and save the extra airport charge?

If none of the above fit your requirements, there is a Hampton Inn, and Courtyard by Marriott just north of Logan with shuttles.

Agree with Myer that you usually can save a lot of money by renting a car outside Logan. Compare prices to see if it is worth it to stay somewhere like Harborside Inn or Courtyard and rent a car from a non-airport location.