As I already said using port knocking to access between two routers is not a “best practice”, you’re over complicating yourself.
If you want to add security use any of the various VPN tunnels available, SSTP is a great protocol for tunnelling between two Mikrotik Routers in terms of performance, security and convenience.
However as the port knocking on the server side is something you should manually achieve by using lists and the various firewall filter rules available, (http://wiki.mikrotik.com/wiki/Port_Knocking) you can get creative if you want to, and craft whichever sequence you like to open the port on the server side, and use Tools > Traffic generator on the client side to send whatever you want, see http://wiki.mikrotik.com/wiki/Manual:Tools/Traffic_Generator
In any case, there’s no pre-cooked or “in built” port knocking feature in ROS neither for the server or the client side.
The best you can do is send a port knock from a PC that’s behind the “client” router, assuming the router is doing NAT.
ROS doesn’t have a packet generation tool - if it did, you could script a port knock, but since there’s not one, you can’t do it.