I use Atmel Studio 6 with the Visual Micro Plugin (both free) for both Teensy 2/AVR and Teensy 3.1.
Excellent.
http://forum.pjrc.com/threads/25757-Q-on-altering-boards-txt?highlight=boards.txt
my post about putting a few lines in the Teensy3 boards.txt file to avoid having Teensy-specific settings in the Studio project.