you will have to use "no snmp-server enable traps syslog" to disable system logging message SNMP notifications, check out the following link for the "snmp-server enable traps syslog" command reference :
http://www.cisco.com/en/US/products/ps6350/products_command_reference_chapter09186a0080444dd0.html#wp1030781
if you do not need syslog traps(which are sent for every message displayed on the console), disable those traps as follows:
router(config)# snmp-server enable traps
router(config)# no snmp-server enable traps syslog