How can I do query level prioritization on MySQL when using InnoDB?

Use a message queue to answer queries.  The easiest thing to do is modify a data access layer to send the queries to the queue.  If you want async queries, have the MQ insert the results into a table that you can access after the query has finished. The most straightforward approach is simply using three queues, each assigned various numbers of subscribes to control how many queries of each type can execute simultaneously.  The high priority queue should have a high number here, such as 80% of the cores in the system.  This ensures that high priority queries are scheduled as quick as possible, and with as much concurrency as possible.  A regular priority queue could then be assigned to the vast percent of remaining cores, while the low priority queue may only be able to execute one or two queries at a time.

No, MySQL has no feature to set the priority of a given thread's queries. Another common tactic, at least for read queries, is to set up a replication slave and run the cron job's queries on the slave.  This doesn't work for writes of course, since you can't write to a slave and have those changes replicate upstream to its master.  But you can at least move some reads off the master.