Gate drive voltage, RDSON, Gate charge, VDS max and VGS max are generally the most important parameters. Your FETs are a fairly close match in all of these.
There is one marked difference between them; the NTMFS489NF has an integrated Schottky diode, while the NTMFS4C03N only has the usual intrinsic body diode. This is reflected in significantly lower reverse voltage drop in the NTMFS489NF; ~0.6 V at 10 A vs ~0.87 V in the NTMFS4C03N (at 25 °C), which will result in less heating when the FET is off and reverse current is flowing.
However in a synchronous rectifier circuit the FET spends most of its time turned on during the flyback period, so the diode is only active during the deadband and should have very low loss. Generally only the lower FET has to handle significant flyback current, so if you are replacing the upper FET there should be no issue. The lower FET might get a bit hotter without a Schottky diode.