If we drive down from Boston-Connecticut to the Manhattan hotel to
check in and drop of the lugguages. Then, return the car to nearby
rental agents. How would you do this?

All the national rental car chains have offices in Manhattan. You can
get a one way rental from wherever to Manhattan, drive to the hotel,
one of you gets out and checks in while the other waits in the car
(they should have bellmen to help with the baggage), then drive to the
rental office, give back the car, and return to the hotel on foot,
bus, or subway.

If you're coming from Boston, Hartford, or New London, the Amtrak
train is a reasonable alternative. You can take a taxi from Penn
Station to a hotel anywhere in midtown and not pay a huge amount.
From New Haven or points south there's the MTA commuter train to
Grand Central, which also has taxis.