Cruise Vessels usually go alongside one of two wharfs in Lisbon dependent upon draught and tonnage. As already noted there is a wharf near Stª. Apolonia where vessels do sometimes go alongside.
However, the main cruise terminal for Lisbon is at the Doca da Alcantara situated next to the 25 Abril Bridge. When I was in Lisbon last week there were at least two +30000t cruise liners alongside.
From Alcantara terminal you have a walk to about 200m to the Lisbon - Cascais railway line where you will find trains (Alcantara-Mar Station) to Lisbon (Cais de Sodre - where you can connect with the Metro), Estoril and Cascais. There is also a tram service going into Lisbon Praca Figueiras - Rossio in one direction and to Belem - Alges in the Other.
If you only have a few hours, take the tram to Praca Figueiras - Rossio which will take you really to the centre of Lisbon.
From there you can see the Castelo, wander up the Chiado etc.
