If I want a baseline in a stream, I prefer to create the baseline directly in the stream, rather than creating it in a workspace and flowing it to the stream, because if multiple workspaces are flowing baselines to a stream, the baseline flowing behavior can be quite confusing (e.g., accepting a baseline into a workspace that has an outgoing baseline can make that outgoing baseline magically disappear).  The simplest approach is to just create a snapshot on the stream (which automatically creates any needed baselines).   But if you want to create a baseline in just one of the stream components, the approach I use is to give the stream a flow target (doesn't matter what flow target), and then you can show the stream in the Pending Changes view.   This will allow you to create the baseline directly in the stream.

This is fixed in 4.0.6, where you can create a baseline in a stream component from the Team Artifact Navigator (see work item Cannot create a baseline on a component in a stream from the TAN (174950)).