1 or 2 nights in Boston -- historic ambiance w/ quality food?

There is nothing like Carbone here unfortunately. I’m not entirely clear on exactly what you are looking for. However from your list above Mamma Maria still does an excellent job and the setting on North Square is rich with history.

I feel Neptune has slipped (https://www.hungryonion.org/t/neptune-oyster-boston-north-end/3911). It has become more of a tourist destination (i.e. will be sitting with lots of people photographing their food). Also my recent experiences are that the price to value has slipped, while the service is still iffy. I’d opt for the newly opened but outstanding Saltie Girl (https://www.hungryonion.org/t/saltie-girl-back-bay-boston-ma/5594) in the Back Bay instead for lunch.

If you’re looking for a chophouse, Grill 23 might check the boxes for you atmosphere wise.