Lisbon have a great transportation system if you don’t count the not so user friendly ticket system. Besides the local bus, tram and trains here there are also ferries that are mostly used by the local people. Instead of taking a guided bus tour or even the “tourist cruise” that also exist here, I recommend you to try one of the normal ferries listed below. All of the boats go from the morning until about 2 o’clock in the night, and usually every 30 minutes even on weekends. The duration of the boat trips varies between 15 and 30 minutes and even though the ride on the river is very calm some minor waves exist that you should be prepared of if you easily get seasick.

Belém to Trafaria

Trafaria is on the other side of the river and from here you can walk about 30 minutes to come to Cova do Vapor which has a magnificent view of the North Atlantic Ocean. This place is also a good spot for wave surfing. Be aware that this is the SECOND stop with the boat, not the first.
Price: 90 cent + 50 cent for the rechargable card (Carris)

Praça do Comércio to Barreiro

This ferry will take you to the opposite side of the river from Lisbon, with the boat ride being almost more interesting than the destination. Barreiro is a fast expanding suburb with not so much to see besides taking a walk along the river.
Price: 1,85 cent + 50 cent for the rechargable card (Soflusa)

Cais do Sodre to Cacilhas

This is a good option if you want to go to the Cristo Rey statue.
Price: ~80 cent + 50 cent for the rechargable card