You keep mentioning a hotel: do you also need a place to stay for the night? Or are you just assuming that anyone can park at a hotel even if they aren't guests? The Longwood Inn you keep mentioning only has free parking for guests; starting at $129 a day (without taxes) for a room is not a cheap way to get parking.

Assuming you are just day-tripping into town, your best balance of cost to convenience is going to be parking at a T station itself. I don't recommend parking at one of the further out ones; the rates aren't cheaper and you'll just be sitting on the T for up to an hour. I think Wellington, as mentioned above, is the right fit of cost to proximity to downtown.