@wholeeverything These are the places that we stayed at that I’d happily recommend
Hotel Museu, Mertola - pretty small town with lots of tiny museums, big castle on top of the hill. Hotel is quite simple but comfortable and great location next to the river, and has Roman ruins in the basement.
Hotel Monte do Vilar, near Beja - great agrotourism hotel in the middle of vineyards, good restaurant. Hotel can arrange a tour of the local wine cellar with wine tasting (they produce their own wine for the hotel chain).
Sines Sea View Hotel, Sines - big modern hotel, good as a stopover. Easy walking into the town.
Praia do Canal, Aljezur - this was our splurge, very modern architecture, beautifully furnished, great facilities and staff. Restaurant food was a bit on the nouvelle cuisine side (ie small portions), but buffet breakfast was huge. Great for activities - lots of cyclists were there, we did a 10 mile circular hike out to the coast.
Pousada Palace d’Estoi - modern rooms in a new wing attached to the historic building. Very handy for Faro.
Also stayed at the Pousada at Sagres, amazing location but the hotel is a little tired, and the Marina Club Suite Hotel at Lagos, which is where we stayed a few times when the DC were small - excellent location.
Alentejo is really pretty - lots of vineyards, olive groves, cork trees, castles, and great walks. The coast between Odeceixe and Lagos is stunning (the Fisherman’s Trail is in our future).