Biomega should be before NoiSE. The Earth is fully covered in Megastructure in NoiSE, from the looks of it and things like the NetSphere, Safeguards and the Silicon Life all exist in recognizable fashions. The City is not yet as large or lonely as it would later be, but it's taking shape.
Biomega must therefore be before that, as the NetSphere doesn't yet exist and the only recognizable faction is Toha Heavy Industries (though the DRF might have later become the Governing Authority, IIRC). The Earth itself is as-yet uncovered and things like oceans and continents still exist. Presumably, the victims of the NS5V virus are what became the Silicon Life. The Megastructure was probably intended to seal them away, growing ever larger as their corruption spread further and eventually growing out of control when no one was left to mind the Builders.