My favorite areas for a hotel stay would be on the harbor or in the Back Bay. Back Bay would be my first choice. Lots of restaurants, shops, and walkable to MFA and all the historic sites. Downtown Boston is very walkable...at least I think it is re: distances, and it is a safe city. What's your budget? I have an inexpensive favorite that I use when I'm doing research in the Back Bay: Charles Mark Hotel and a more expensive one when I want to be more pampered at which I can use my Avios: Fairmont Copley. For the harbor and harbor location I would pick either the Marriott or Boston Harbor Hotel, which I prefer, but I don't suspect they are inexpensive suddenly. Even if you don't stay at the Boston Harbor Hotel, you might want to have lunch outside on their terrace...assuming you are going in warmer weather. Or relax and have a drink while watching their outdoor summer movies. Also, eat in the North End once as well, one block off Hanover Street.
Base on your Holiday Inn Express comment, I think you will find the Charles Mark Hotel fine. As I said, I often stay there, but not since Covid. It's a little more European with small rooms, but the price is lovely and the location is great. Boston has been a great city to walk around since at least the mid-1970's when I arrived.
Any terminus of the subway has parking or those I know anyway. Just check the rules for overnight parking as I don't know them. My preference would be to not stay outside the city, just leave your car outside. If you don't want to do that, an easy trip into the city would be from North Quincy T stop (15 minutes) and stay at the Best Western Adams Inn, Quincy, which will shuttle you to the subway, although it is not a hard walk, just not pretty... Also, if in Quincy, there is the National Adams Historic Park which is a very nice visit to the homes of the Adams Presidents, etc.