We have an issue when a user is infected with a virus that floods the interface with very high pps counts of icmp or udp on the order of 2200+ pps which causes the interface to virtually stop.
We can access the router fine, but in order to stop the offending user we need to get to the segment they are on and it is effectively disabled by the attack.
Is there a way to limit the max pps per ip? I have looked around the forum with no luck.
Has anyone had this issue? Any help is appreciated.
Thank you.

use queues. I suggest pcq queues, if you want equally limit bandwidth between users:
http://www.mikrotik.com/docs/ros/2.9/root/queue

Is there a way to limit the max pps per ip? I have looked around the forum with no luck.
Has anyone had this issue? Any help is appreciated.

Yes, many times, until both ends ran something that could filter or aggregate those packets on the offending end.