It would seem that yes: there are still leap years
Memory Beta doesn't have much to say on the matter unfortunately.
According to Memory Alpha:
One Earth year was equal to 365.2425 Earth days in the Gregorian
calendar. To compensate for the fraction of a day, a leap day was
added to every year whose number was divisible by four, unless it was
a century, unless it was divisible by 400. These leap years consisted
of adding an extra day to the month of February. Instead of the usual
28 days, there would be 29.
Now, this explains the situation as it currently stands; because there seems to be no mention of removing leap years, we could assume that they still exist.
Furthermore, the introduction of Stardates did not impact our local Earth calendar:
Stardates did not replace clock time or everyday units for expressing
larger timespans, such as days, weeks, months, years, centuries, or
Hence, it would seem that there has not been any modifications made to our current calendar system in the Star Trek universe, at least none mentioned which would impact the presence of a leap year.