Sorry to chime in so late, but I second the bid for Porto...a great city and the North of Portugal is both beautiful and fascinating. It has been many years since I have visited the Algarve but between the other two tours I would opt for Silves, Lagos and Sagres, mainly because all three of them, most particularly Sagres and Silves, are particularly interesting historically and, as a former history teacher (which I am, as well), I believe that you would find them very interesting as well as very colorful.
I envy you your visit to Lisbon, probably my favorite city, and the fall is a great time to visit. If things work out it is very possible that I will have been there and gone by the time you arrive. Don't neglect to spend one day visiting Cascais, the heavenly Sintra and, among other attractions of Lisbon, the palace at Queluz, where you can lunch at Cosinha Velha (The Old Kitchen) which belongs to the Palace. Although there are a number of fine museums, the Gulbenkian remains one of our favorites.
I am certain you will discover some of the finest restaurants such as Tagide, Pap' Açorda, Sua Excelencia and others...but let me add a small and very special one called "Nariz de Vinho Tinto" (Nose of Red Wine) just around the corner from the Hotel Lapa.
I hope you plan to hear some fado . There are many fine clubs, but for a great introduction I suggest "Senhor Vinho" and " Parrarinha de Alfama" both with good food and really fine fado. The first is a bigger and slightly more commercial venue but it has the real feel of an "adega tipica" (fado house) and presents some of the best singers, while the second is a smaller, more typical venue whose owner, Argentina Santos, still sings most weekends and is one of Portugal's oldest and finest living fadistas (fado singers.) Another excellent club used to be called "João da Praça because it's at 92/94 Rua João da Praça, but they've changed the name. Your tour guides will know it.
I hope you all have a wonderful trip. Don Cohen in Los Angeles