Yes they probably will go up. Your best bet is to call the township, explain what you want to do, then speak to someone who can explain how they base the property taxes on new construction, even is you leave the same footprint and/or square footage.
732-248-7200 main number. 732-248-7211 tax assessor
Remember, your contractor/builder is going to have to file plans and apply for permits. Typically you need to have the plans approved, then each step (framing, plumbing, electrical work, even insulation etc) will have to be inspected and approved prior to moving onto the next step.