Luckily, I have been working with a colleague on a knowledge document indicating queries that retrieve from the database a list of users with the "Last Login" timestamp. You could use the queries there and do some adjustments to get only users that haven't logged in on the last 90 days.
As you can see, it lacks tests on other supported databases for JIRA 6.3+, like Oracle and Microsoft SQL Server, that's why the KB is still unfinished. If you use one of these databases, some adjustments to the queries' syntax should be performed.
Let me know if you have any doubts on this. I'll do my best to help out.
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