Since installing the new NAM, My ferries are not working. I use Pegasus's ferry terminals
Try the Maxis ferry terminals and see if that works. PEGs ferry lots seem to have some quirks regarding the placement, as described in the readme file.
When I placed the maxis ferry, the game crashed.
The ferry crashing issue was an issue with the May 2010 version of the NAM (Version 28). It was resolved with the current release of the NAM (Version 29 from August 2010). If you are still having ferry crashing, you have an outdated Controller file from the previous NAM. Make sure you remove all outdated NAM files.
-Alex