Tuning PID without transfer function
If you don't 'know' the transfer function but you can run experiments (on simulink) with it you can either


Determine an approximation of the TF using an ARMA model or other system identification techniques.
Use a genetic algorithm to tune the PID until you get a 'good' PID for that system.
Use methods such as the Åström-Hägglund relay method, a self tunning method.
Use Ziegler-Nichols method to get some controller.