First you have to make sure you can even do it in the first place. You have to look at the zoning to see if a three family dwelling would be permitted. You need to speak to an architect and maybe even a lawyer to help you. The legal cost of the conversion alone would be about $10,000 in Brooklyn and that does not take into consideration any physical changes that you would have to make in order to do the conversion. There are many safety codes a three family has to meet that a two family does not. All along the process the city will also have to come and inspect and if anything is not to their liking you will have to fix it. It may open a big can of worms.
Also, if you want to add another heating system, it has to be done by a licensed plumber/electrician and you are talking about $5,000 minimum and you also have to have enough space to do it. It would be a lot easier just to purchase a legal three family.
If you need a recommendation, I know some architects and lawyers if you need. If I can be of further assistance, please let me know. Good luck!
Mitchell S. Feldman
Associate Broker/ Director of Sales
Madison Estates & Properties, Inc.
Office: (718) 645-1665/ Cell: (917) 805-0783