Per my answer to this question, yes there are levels of canonicity. These are set by the studio as well as there being broad agreement across the more (ahem) avid fan base.
1) The TV episodes (TOS, TNG, Voy, DS9, ENT) and the 12 films are the highest canon (as well as transcripts, deleted scenes, Animated Series and the various IDW (ongoing) Comics, where they don't conflict with what happened on screen)
2) Original scripts (which may or may not mirror what actually happened on the show)
3) Interviews with the writers and producers, cast and crew (AKA "Voice of God")
4) Canon reference books such as the "TNG Technical Manual", "DS9 Technical Manual", and "Voyager Technical manual". These were originally written as reference manuals for potential script writers.
5) Non-canon reference books such as "Mr Scott's Guide To The Enterprise" and the "Starfleet Technical Manual". These were written by people closely associated with the show but may have been contradicted later. They're usually considered 'canon unless otherwise contradicted'.
6) Official novelisations of various episodes except where contradicted.
7) Deleted scenes where they do conflict with established canon
8) Officially licensed properties such as the Star Trek Games, RPGs, Crossover-comics and Trek comics produced prior to 2012.
9) Expanded-Universe Star Trek books. Those written by those involved in the show (such as Bill Shatner, Jeri Taylor and Armin Shimerman) are generally considered more worthwhile than those written by people with no involvement in the show.
10) Fan-made properties such as Star Trek: Phase II and fanfiction