Do I need permission from my ex husband to take our daughter to New York for 2 weeks on vacation?

You need to look at the final judgment giving you joint custody. It should answer your question. If it is silence in the matter, then the answer is yes. You will need a signed affidavit giving you permission to take your daughter out of Puerto Rico. Even if he gives you verbal permission, you should get the affidavit anyway to protect yourself. Good Luck.