The Puppet Server 1.x series is targeted for use with Puppet 3.x agents (and uses the Puppet 3.x catalog compiler). The latest version of 1.x at the time of this writing is version 1.1.1, which should be available in the main Puppet Labs apt/yum repos:
You should be able to try this out in your current environment by simply (temporarily) stopping the service where you are running your Passenger-based Puppet Master, and installing the 'puppetserver' package. (Not a bad idea to try this in a test environment first, if you can... and if you are doing anything complicated with your Puppet CA you may need to take a few additional steps.)
If you try this and it doesn't work for you, you should be able to simply stop the 'puppetserver' service and restart your Passenger-based master.
The Puppet Server 2.x series is where we introduce support for Puppet 4.x agents and use the Puppet 4.x compiler. These packages (along with Puppet 4.x itself) are in the new 'Puppet Collections' repos:
Puppet Server 2.1.x and greater should still be able to handle requests from Puppet 3.x agents, but will use the Puppet 4.x compiler, so may require changes to your manifests.