We own an aparment in israel and visit for Chagim. our primary address is in the USA. we hold one day yom tov. is there any problem leaving on Motzai Chag in Israel irrespective of what time it is in NY?

Since you conduct yourself according to the opinion of the Rabbis who hold that one who is in Eretz Yisrael during the 3 Regalim is considered like a Ben Eretz Yisrael and keeps one day Yom Tov, you are considered a Ben Eretz Yisrael regarding this law. And the law is that it is permitted for a Ben Eretz Yisrael to leave Eretz Yisrael and go to Chutz La’aretz on Yom Tov Sheini Shel Galuyot. However, it is prohibited for him to enter the Tchum [2000 Amah = about 1 KM] of a Jewish settlement on Yom Tov Sheini itself. Nevertheless, if there is a possibility that people who see you may think that you are desecrating Yom Tov Sheini [especially because your primary home is in the U.S.] this may lead to disrespect of Yom Tov Sheini Shel Galuyot. Therefore you should make sure not to enter the Tchum of a Jewish settlement on Motzaei Yom Tov until after the time it would take to arrive if you would leave Eretz Yisrael on Motzaei Yom Tov Sheini. [שו"ע ומ"ב או"ח סימן תצו סעיף ג ובפסקי תשובות שם וע"ע בספר יו"ט שני כהלכתו]