My impression is really that the OP is looking for books that could be considered and enjoyed as great scifi novels independent of the franchise association, i.e. the question is less about quality in an absolute sense and more about quality sans context.
As in, a Star Trek
book can be a great Star Trek
book because if makes effective use of or subverts characters/situations/tropes from the franchise, but that makes its greatness dependent on that context, whereas some stories may be set in the franchise, but mostly do their own thing. Many of this latter category then come out as lackluster because that own thing just isn't very good and they also don't tap into anyone else's good things - but some are also shining jewels.
The ones that come to mind easily are The Final Reflection
and A Stitch in Time
, which make really worthy social scifi tales even if ripped out of the greater tapestry of the Star Trek
franchise. Quite possibly also Crossroad