When discussing Animal Logic's involvement in the film, they state:
Initially, Production Designer Grant Freckelton and his team utilised LEGO Digital Designer [...]. This allowed everyone, including the Animal Logic art department, to mock up highly accurate LEGO models from which they could calculate the required bricks and build them as subdivision surface assets.
These LDD models where then converted to an internal format that works throughout Animal Logic's pipeline, at which point the could start using their more usual tools:
The bricks themselves were separately modeled in Maya, with asset and layout builds achieved in Maya and XSI.
A pull-quote from an FX-Guide article on the work notes:
Animal Logic’s main toolkit relied on rigging, layout, animation and lensing in Softimage, with surfacing, lighting and rendering done in Maya, MARI and RenderMan and a custom renderer called Glimpse. Effects work was handled in Houdini.