I hope you are still interested in the subject even though a month has passed since you posted your question.
Bonkowski and Bąkowski (Bakowski where "a" has a tail) seem to be variants of the same name because their pronunciation is identical, whereas Bunkowski may be a misspelling of Bonkowski, which has been used after the wrong spelling was recorded.
The root of Bąkowski is Bąk, meaning "bumblebee or horsefly" or "bittern" (a bird)
Bonkowski can also be an alternative spelling of Bońkowski where the "n" has a mark above. It originates from a place name Bońkowo which itself is derived from a given name Boniek, short for Bonifacy.
In 2002 there were 3345 individuals using the surname Bąkowski living in Poland:
Here is map of the distribution of the surname and the number of people using it in Poland in 2002:
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