This all depends on what you want to focus on. From your question, the thing you are most interested in is the data flow throughout the different layers (user-space stream -> voltage on the cable).
For this, I propose you use http://www.csse.uwa.edu.au/cnet/, which is a full network simulator. It allows you to step through all levels of the stack.
Real systems will always have a clear distinction between Layer3, Layer2 and Layer1 (Ethernet and CRC-checking firmware on chip, hardware MAC). You will have trouble getting into the OS and some implementation details will be messy and confusing for students. For Linux, you’ll have to explain kernel infrastructure to make sense of the TCP/IP stack design.
If you are only interested in the TCP/IP part, I recommend you use an embedded TCP/IP stack like http://www.sics.se/~adam/lwip/ . You can incorporate this into a simple user-space program and fully construct the TCP/IP packet.
Please note that there are a lot of network communication aspects that you cannot address while stepping through the TCP/IP stack. There is still a MAC chip in between which regulates medium access, collisions etc. Below that, there is a PHY chip which translates everything into electric/optical signals, and there is even a protocol which handles communication between MAC and PHY. Also, you are not seeing all aspects related to queueing, concurrency, OS resource allocation ea. A full picture should include all of these aspects, which can only be seen in a network simulator.