Using the ferry to see Loreto:
Loreto by Ferry: the port of Los Mochis, southwest of Hermosillo or a few hours south of Puerto Penasco (Rocky Point) is the mainland terminus for the ferry that comes to Santa Rosalia, located about two hours north of Loreto (see its description elsewhere in the site). To the south, La Paz has a terminal at Pichilingue serving ferries to Topolobampo, and also to Mazatlan, an overnight run to the southeast. Remember on all of these that US plated cars, although you can drive them right down the Baja and back without a permit, require a permit to enter mainland Mexico. You have to get that in advance, so don’t get caught in an embarrassing situation (not being able to get on the ferry). Under no circumstances should you drive a car that is titled to someone else to mainland Mexico, ferry or otherwise.
There is scheduled ferry service between Santa Rosalia (3 hours drive on Mex. 1 North) and Topolobampo, Sonora each week on Baja Ferries. The one way trip takes approximately 6 hours. Baja Ferries also has scheduled ferry service between La Paz (5 hours drive on Mex. 1 South) and Los Mochis, Sonora (5 hours) and Mazatlan, Sinaloa (16 hours).
Baja Ferries
http://www.bajaferries.com/