The official line from Altera is:
"In the past, Altera produced a simple, proprietary networking stack called PLUGS for use with the Nios I processor. This stack was created out of necessity because (at the time) there were no other readily usable, cost-effective alternatives which we could provide to customers. PLUGS, however, was never a functionally complete networking stack and never fully implemented the TCP/IP protocol. With the release of the Nios II processor, a conscious decision was made to provide users with a super-set of the functionality found in the Nios I development system, networking stack included. During the Nios II development effort (c.a. 2003), we found that an open-source networking stack existed called Lightweight IP (LWIP), which was far more robust in protocol support and compliance to existing network RFCs. In order to provide our customers with the best possible networking stack solution for the Nios II processor, we decided to drop our existing PLUGS networking stack and adopt the LWIP solution. All Nios I customers migrating to the Nios II processor are strongly encouraged to adopt the LWIP solution- they not only will get continued support and bug-fixes for this stack from Altera, but also their applications will also benefit from the services provide by a robust networking stack. Customers wishing to use the PLUGS networking stack on the Nios II processor do so at their own risk."
In short if you want a fully functional Altera supported TCP/IP stack, you will need to migrate to LWIP. In particular, you will need to do this if you want reliable TCP.
If you are only using a subset of the available protocols, then it is possible to configure LWIP so it doesn't include unecessary code. When using the MicroC/OS-II version this is done through the "Software Components..." button on the system library properties page. Note that additional options are available if you expand out the "Lightweight TCP/IP Stack" option on the left hand side of the window.
Options that are particularly important in terms of code footprint are the "Memory Options". You may also want to consider disabling TCP support if you are only using UDP (for example).
These same options are also available for controlling footprint when using the standalone version of the LWIP stack. I'm not familiar with how those are presented, but I imagine that they are set in the lwipopts.h file.