There is no "best way" travel from Porto to Albufeira. The distance between the two centres is +- 550km.
The options are:
1) Car.
Advantages - Motorway all the way.
Disadvantages - Price of fuel and tolls on the Motorway.
2) Train
Advantages - Two direct through trains per day
Disadvantages - Price is higher than bus and the station is at Figueiras 8km from Albufeira meaning one requires a bus or a taxi to get there.
3) Bus
There are two bus companies offering services.
Renex
Rede Expressos
Both require changing buses in Lisbon.(Same bus station)
Renex is probably the cheapest option of the lot.
4) Air
ryanair.com now fly twice daily between Faro Aiport, 40 km from Albufeira, and Porto.
Flight time is one hour.
However, it is a hassle getting direct from Albufeira to Faro Airport. It requires a taxi, private transfer or a bus!
For links to most of the companies mentioned above, go to my blog here:
http://barlaventostravelblog.blogspot.com
Scroll down on the right hand side and you will find a panel entitled:
Algarve & Portugal - Travel Transport Links