DW and I spent an anniversary night at the Seaport Hotel on the waterfront...it wasn't expensive at all ($129 for a harborview room with King bed, $99 for a non-harborview), very nice and comfortable, sort of business oriented. The only problem it wasn't really in a great "walking" location. It did have a nice sports bar nearby (Atlantic Beer Garden - watched the Patriots there) and a pricey but nice steak house (Morton's) right next door.
There is a Silver Line T stop right nearby, so you can hop that to South Station to get to the rest of the system (or walk from there).
I work right next to the Seaport hotel. It's a very nice hotel but agree that it's not the most convenient place to stay. In the spring/summer time it's great since you would need to walk or take the T every where. I would look at the Omni Parker House. You are close to everything here and it's a historic hotel which is nice.
One of my favorite places to eat is Parish Cafe. They have great sandwiches (it's sit down resturant) that chefs from across the city have developed.
Plus you can't go wrong with the North End. I have never had a bad meal at any place.
Finales also have the best Desserts.