I highly recommend staying at Second House, we had a very enjoyable experience there.
Pros: Very large space, it feels more like a house (on 3 levels) than an apartment. The layout includes a bedroom on the same floor you enter the apt. on, with an en-suite full bathroom. There is also a 1/2 bathroom next door. Also on that level is the lovely patio. Up a few steps are the other 2 bedrooms, one with a double/queen (and a crib), the other with a single bed and a child's bed, and another full bath. Downstairs from the entry level is the spacious living room with large couch, TV, etc, the dining room, and the well-equipped kitchen.
There are room-darkening drapes and A/C units in each bedroom.
We loved the location in the Barrio Alto, which is full of winding narrow streets, colorful houses, countless bars and restaurants. The house was surprisingly quiet at night, given all of the late-night activities right down the streets nearby.
The host responded rapidly and helpfully every time we texted her, she went to much effort to solve an A/C issue we had. Overall, we loved Lisbon, and loved this house.