Robert,

correction for emissivity is done by measuring several (three usually)
bands. If the source is sufficiently diffuse it will not be fooled too
much. Afaik, if you try to read a temperature through something then you
need to correct for the something. In other words, measure temperature of
transparent something, and measure inside the something transparent. Then
you process the second reading to obtain the correct reading for inside.
The formula involves the transmittance of the transparent something for
the radiation of the inside something. Both temperatures must be read with
the same kind of instrument and preferrably with a parallel beam (using
refractive infrared optics).

Peter

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