Our decision in 2006/7 was between Lagos and Portimao and, having visited both, Lagos won by many miles, for so many reasons. Portimao was a little cheaper for the 9 month deal, but it was no contest.
So my vote would be for Lagos
Never been to Villamoura but, having heard descriptions, never felt the need.
Portimao is cheaper on price especially in July/August
Vilamoura is closer to Faro- the local airport
Vilamoura is heavily populated with golfers for over half of the year (you decided if this is good or bad)
Vilamoura has more bars in the marina, this has its advantges in the winter but means no sleep on board until about 0400 in the summer months as the marina is a very noisy place.
I have not been tp Port Mao but have been to Villamoura, I thought that Villamoura was great perhaps a little too touristy but if you want bars and eating establishments you will not be sad.
I also seem to recall bars closing down early, cant remember very late nights
I don’t have a boat there but I do visit both Vilamoura and Portimao several times a year. Vilamoura is about 20mins by taxi from Faro airport, Portimao about an hour. Vilamoura is a purpose made resort, popular with golfers. This means there’s some life there all year round but it can get very ‘lively’ during the peak season. The bars and restaurants around the marina are not bad pricewise but not cheap either, especially with the pound as it is. There are no big supermarkets near the marina but the nearby mini-marts will have most of what you’ll need.
Portimao marina is quiet, very quiet. There are only a few restaurants/bars on the marina and some of them close out of season (the season being much shorter than in Vilamoura). There are plenty of cheap bars and restaurants in Praia da Rocha but it’s a slightly tacky seaside resort and there are a lot of steps up to the strip from the marina. Portimao itself is a dump and best avoided. Large Aldi and Continente supermarkets are about a 5 euro taxi ride from the marina but smaller shops are within an easy walk.
The Portuguese are fussy about VAT paid status. Make sure you have all the paperwork. If you buy a new boat they will insist that you pay Portuguese VAT (21%) even if you already paid VAT in another EU country. There is also a local annual tax based on engine horsepower but UK flagged boats can avoid it by staying in Spain once or twice a year (Ayamonte is popular for this).
Finally the water off the coast is always cold.