Noticed that my divorce stipulation and divorce decree are different regarding end dates for child support. The decree appears advantageous to my position and the stipulation to my ex-spouse. Does one formal document trump the other? If so, what methods of recourse does one have?

In NY the decree overrules the stipulation.

Before the decree is filed - has it been filed yet? - the discrepancy should be brought to the attention of the Court. You could have problems down the road if this isn't resolved now, problems which will cause you to have additional legal fees.