I would precess MODIS images on QGIS (in particular swath images MOD09A1). I use MODIS Reprojected Tool Swath to trasform .hdf file in GEOtiff but there are different avaible bands (16) and i don't know what are the reflectance bands number 2 and 7. I would process these band in QGIS to elaborate NDII index.
Check out the MOD09 user guide here on page 17 it lists the bands in the MOD09A1 product and their wavelengths.
From that information you should be able to decide which bands you need to use in your Normalised Difference Infrared Index (NDII). Having never done an NDII I would have thought band 2 and 6 would be required looking at the formula for NDII mentioned on this page.
Get the two bands that you determine are correct for the NDII into QGIS and you can use the Raster Calculator to create your index.