You stated that you were never married to the father. Is his name on the birth certificate? If not, than you don't have to worry about it since as far as the cruiseline is concerned she has no legal father.
Also, you mention that you have custody of your daughter. Do you have legal custody of her or only physical custody? If you have sole legal custody than you do not need anything from the father unless the court paperwork specifically prohibits travel without his consent. Generally, sole legal custody gives you the right to make all decisions regarding the child (including the right to travel). Physical custody only determines who the child lives with.
If you do not have sole legal custody than you can go to court and ask a judge to authorize the travel. Being that the father isn't around to oppose it, the judge should grant your request easily. You might also want to look into having the original agreement changed to give you sole legal custody if you don't already have it. Again, being that the father isn't around to object, this probably wouldn't be that difficult to do, although it is a little more involved then just getting a judge to grant travel authorization.
All that being said, based on my experience, there is a very good chance that you will never be asked to produce any documentation at all. I have been on many cruises (including 2 this year) with my single-parent sisters and their kids and never have they been asked to produce any evidence that they have the right to take the kids out of the country (although they did have the evidence with them). This is true even though the kids all have different last names than their mothers and even though one of the kids is black and the rest of the family is white (she's adopted).