Should I use time machine to migrate from one mac to another?
The best way to do this is with Apple's Migration Assistant. Plug the Macs into each other with an ethernet cable and launch Migration Assistant on both. Follow the instructions on screen.

I've migrated to new machines seven times and it's a pretty flawless system. Based on other answers I'm pretty sure that Eclipse won't really know the difference after migration as long as your short name on both Macs is the same.