Sure.
Polycarbonate, Acrylic and PMMA are all perfectly fine coverglasses. Near I/R Photons go right through them.
But there is a limit. Try to design your coverglass so that it's as thin as you can make given your other constraints.
And try to jam the sensor as close to the glass as you can get it.
You will get some crosstalk - but it can be calibrated out.
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