Both vocabulary and ontology refers to a thing. Although they have differences.
Vocabulary
Vocabulary is an understanding of what a thing is.
Example:
Apple is a fruit. Apple is also a shortname for the company Apple Inc.
Ontology
Ontology is the overall understanding of a thing with regards to its relationships, similarities & differences to other things.
Example:
Apple -> is a fruit -> produced by an apple tree -> which has a scientific name -> Malus domestica -> Of which, Apple Inc. -> got its name
As to which is preferable, since you are working with semantic web and linked data technologies, ontology will make more sense to you.
Vocabulary was what machine learning laboratories derived from processing information on the web. Machine learning on that direction is not going to cut it. People from W3C realized it and that to understand things further, Semantic Web and Linked Data were some of their solutions. Which gave rise to this complicated notion of ontology.
Vocabulary is much more easier for human beings to comprehend while ontology is easier for the machines.