Considering the rubber dissolved in a non polar solvent, I would guess a polar wash would not get rid of those products. The safest way would of course be to discard everything and take it as hard learning...Thats the recommended... Next time use glass or hdpe only! If you anyways decide to use it, then better salt out, rebasify, re-extract and then freeze precip and recrystallize the final product, even more than once. Better safe than sorry
A glass syringe can be perfect for this IMO, you can fast and acuratelly pull large quantities of solvent if you have a, say, 50 or 100ml syringe. Its all made of glass and its just two parts that separate and are very easily cleaned.
Also it can be a good trick to first crudely separate the top layer with maybe a bit of the black stuff to a thinner container and then accurately transfer/syringe/pipette out to the final container.