My son is carrying my last BF's surname, can I take my son without his father's

[RobsLuv]

CIC will require that you either have legal documentation of your full physical AND legal custody of your child, or written and notarized consent from the other biological parent.  They are not going to accept an explanation that you haven't seen them for years and don't know where they are.

If someone is in this position they should petition the Court for full physical and legal custody due to abandonment - BEFORE filing for PR.  CIC is very specific about all custody issues being resolved before you file that application.  So get a court document saying that you have full legal and physical custody of your child, or get consent from your former partner.