They are very different things: Workspaces runs a full desktop environment (Windows or Linux) on an EC2 instance, and enables you to remotely access it through client software. The client software uses Teradici PCoIP, rather than VNC or RDP, and Teradici is amazing: it is so fast that the desktop feels like it is running on your local computer.

This means that you can run whatever development tools that you want on the EC2 instance, rather than the very limited code editor that Cloud9 provides. You can easily run a full copy of Visual Studio on a Workspace, and get the full resources of an EC2 instance with SSD drivess.