Shahaji Bhonsle is the biological father of Chhatrapati Shivaji.
There are innumerable sources for this, two are mentioned below:
Without any facts and evidences, James Laine in his book claims a Hindu Brahman scholar and Shivaji's teacher, Dadoji Konddev as Chhatrapati Shivaji's biological father. Laine does not calim any Muslim as his father.
Laine cites following source for his assumption: (on page 93 of his book.)
Maharashtrians tell jokes naughtily suggesting that his guardian Dadoji Konddev was his (Shivaji's) biological father.
Now, this book does not make any such claims and James Laine has apologized for his mistakes.
And claiming some muslim pathan as a father of Chhatrapati Shivaji is nothing but a propaganda to maligning his great image. And all such claims are factless.
Shahji was a general and later regent of Nizamshaha, a muslim ruler in Ahmednagar. Marathas treated everyone equal and never discriminate on lines of caste and religion. So, Shahji worshiping a muslim saint or Chhatrapati Shivaji employing muslims in his army is no surprise.