I believe the .vqm writer is being discontinued for newer families, so that won't be an option going forward. It's also pretty susceptible to reverse-engineering since it's a structural verilog(you could argue everything is, depending how much time they want to put into it).
Another option is to export your design as a partition. The user could just import that into their design. It's a little more "strict" on how it needs to be hooked up since it won't go through synthesis again, but the .qxp file is a binary that stores information in the langauge of Quartus's database, not a known format like verilog. They both have their pros and cons.