I've been doing both recently - I'm using Netbeans, and was initially frustrated by the lack of control of generated code. I then discovered that you can add custom code from the GUI builder, which overcame most of the issues. However, I became more frustrated by the layout manager in NetBeans, and found this was hurting my productivity more than anything. I've switched to using MiGLayout and doing most of the coding by hand now. Having said that, NetBeans overall is pretty good, and perhaps I should have spent more time learning the GroupLayout.
If you are doing team development, make sure you are all using the same tool if relying on a GUI builder.
