ModTweaker's Thaumcraft integration extends the command palette provided by CraftTweaker.
To access these commands you do the same as you do for CraftTweaker commands, you use the /crafttweaker prefix

List of Thaumcraft's Commands

Link to list-of-thaumcrafts-commands

Usage:

/crafttweaker thaumcraftDump

/ct thaumcraftDump

Description: Dumps all the Thaumcraft information to the crafttweaker.log file.