The personal tax instalment that is due on June 15th is still based on the personal tax return that you filed for the 2015 taxation year. The instalments that are due on September 15th and December 15th will be based on the 2016 tax return. This fact makes it more complicated for taxpayers to figure out what they should do.
My general advice always is, if Canada Revenue Agency asks you for money, you should give it to them. One should be very certain that any bill is not owing before you skip making a payment. Since the amount of money you are going to make in 2017 is as of yet undetermined, you should pay the installment that CRA has requested. You will not be charged interest or a penalty as long as you pay the amount they asked for – no matter how much you end up owing for this year.