hi Carlos
For wireless client packets and the GRE tunnel you can use the sap mtu, the controller will automatically perform tcp mss adjustment based on the calculation of the sap mtu minus the overhead of the protocols in the tunnel (including the wlan encryption). Confirm the current value with "show datapath tunnel".
The controller vlan interfaces also support MTU chaning if you are talking from a mangement perspective, they also support PMTUD - you shouldn't have to change them.
finally, the last place you can change MTU is if you are running PPPOE connection to the controller for management purposes, this is done via the vlan interface where PPPOE is setup, under ip pppoe-max-segment-size.
regards
-jeff