Hello,
You can check the available modules with the following command: syslog-ng -V
Probably you will not find mongodb in the list of modules.
If you compile from source syslog-ng try to detect the mongodb client header files. If it doesn't find a proper one, syslog-ng will be compiling without the mongodb destination driver.
So you have to install the proper header file and compile syslog-ng again.
If you use ubuntu/debian distro the following command may help: sudo apt-get install libmongo-client-dev
I hope it helps,
Br,
Laci