I regret that at present there are no regular or charter coastal passenger ferry type services skirting the Portuguese Coast.
A car hire Is possible but if you are coming this summer be aware that the roads will be very busy and the climate hot. (35º to 40ºC). If you are not used to driving in temperatures like these you really need an air conditioned car.
Faro to Porto by the shortest route (motorway) according to Michelin is 550 kms. Without stops this equates to 5hrs. 30 mins. With stops you need to allow at least 6 hrs. 30 mins.
Note that both the main motorways are toll roads and in addition to fuel you would have to spend at least Euro 70 on tolls. (euro 35 each way.)
If you want a car I recommend this company - Luzcar:
http://www.solpraiaferias.com/carhirealgarve/index.php?option=en
I have know and rented from them for years.
My opinion is that if you want to visit Porto take the train.
The early morning service from the Algarve (Faro 06:55) gets you to Porto at 12:44. You will see a lot of Portugal on the way and it is very comfortable.
You can then have two nights in Porto and come back on day three.
