Linux or Windows? Which one of altera's software is more stable?

Linux Ubuntu (unsupported OS version, but works). Only issues if you have an old USB T-Guard for your license. (No longer officially supported in either version but not supported at all in the Linux world).

Like Linux because it has less OS overhead, and you can control it easily. It's also easier to deal with multiple tool versions in Linux -vs- windows.

I currently have four versions if Quartus installed with Modelsim ASE along side Modelsim DE and Aldec Riverera Pro with no issues using a "module load" to load up what ever version I need.

This is a must for me, working with multiple customers with different tool environments.

Pete