I would recommend SCaVis (Scientific Computation and Visualization Environment). First, it is Java and runs on any platform. I has a nice editor and you can program in 4 scripting languages (including Python, Ruby). The graphics includes 3D. There is also about 300 examples and very extensive SCaVis online manual which covers

• Functions (parametric, not-parametric)
• General math (integration, differentiations)
• Linear algebra
• Data analysis, mining, histograms
• Statistics
• Symbolic calculations

and all of this can be integrated with plot canvaces in 2D and 3D.