I have my office in NJ but have a choice to live either in NY or in NJ. Which is a better option from a tax perspective ? Does NY have higher taxes than NJ ?

NJ has lower taxes, so living and working in NJ will save money over living in NY and working in NJ. This is especially true if you are considering living in NY City or Yonkers, as you would then have to pay both NY State and NY City (or Yonkers) income taxes. Also, don't forget the savings in the lower cost of housing in NJ as well as lower commuting costs, time, and hassle.