I would like to strongly recommend Margarida's apartment. I will describe my experience as follows:
1. Great location - not in the city center but close to it. The neighborhood is calm and quiet. You have access to cheaper local restaurants, bars, shops where you can meet locals, see how they live, how they drink "um bica" (Portuguese name for espresso) in the morning.
2. The old town/city center is easily accessible by tram and bus - during the day and night (there is a direct connection during the night so no taxi is needed)
3. The apartment itself is beautiful, spacious, well equipped and clean
4. Margarida is a nice, communicative, helpful and flexible person.
To summarize - you can't go wrong with Margarida's apartment!