If I understand your explanation of the property correctly, it is a 3 unit property, but consists of one 2 unit and one single unit. That is where you have the problem. Fannie Mae guidelines require there to be exact comps if it is a property like that which is a-typical. From your comment about not finding comps, that is probably the issue. I have no idea why a credit union, who typically don't even do FHA loans, told you that you cannot have a non-occupant co-borrower. Clearly someone who is your father is a relative, so obviously that is not the issue. The other issue is ownership interest in a property that is only 15 miles away. No matter what you try to say about your reasoning, anyone will give you a problem with that one unless you show from tax returns that you are currently renting out that property.
How much do you have for a down payment? You may be able to get a loan from someplace like Ulster County Savings Bank, if you have enough to put down for their guidelines, and you can get over the hurdle of the other property. Because they generally don't sell to Fannie Mae, they would be more likely to go with an odd property.