My wife and I are not living to gather. Have not done a legal separation yet, only temp custody and child support. She now has custody. I just found out from the kids during a visit that they have moved out of her place and moved in with her boyfriend. I live in NY. I need to now if I have a say on the kids living with him. I an planning to begin the divorce soon and am planning on going for custody.

No, you don't have a say, unless there is something provable about him that is damaging to their safety, such as drugs and a criminal record, and for that you would go back to court to present it, as well as tell your divorce lawyer.

I'm not sure of the NY laws, but in California, if the kiddos witnessed Mommy having sex with the boyfriend, that could cause a custody issue, besides the criminal past and drug use mentioned by joypulv above.

Apparently you have a legal separation. So yes she is free to move in with whoever she wants. However, in the divorce, you can bring this up as part of a custody hearing.