Yes, you can vary the VCCIO voltage to any voltage within the VCCIO minimum and maximum values specified in the "Device Recommended Operating Conditions" section of the data sheet for the MAX® series device you are using, including switching to a different output voltage within the recommended operating conditions. For example, with an EPM7032AE device, you can vary VCCIO between 2.3 V and 3.6 V.
The output buffer voltage of the device increases or decreases as the VCCIO voltage increases or decreases, respectively. However, Altera® does not guarantee the output voltage to be a linear function of the VCCIO voltage.
To make sure your design operates as expected, perform timing simulations for the different VCCIO voltage levels you plan to use.