I’m guessing you already found Harvard Law’s webpage giving information about how to satisfy the NY 50 hour pro bono requirement. It’s directed at law students but a lot of the info also applies to practicing lawyers.

You should be able to do pro bono work “on your own” if it’s through your firm, and then have some attorney at your firm complete the certification (like the pro bono partner if your firm has one, or the partner technically assigned to the pro bono case(s) as the overseeing partner, or your office managing partner). But if you mean doing pro bono work “on your own” by just doing some pro bono work unconnected to your firm, I would check with your firm’s rules on that first as most firms won’t let you do any legal work for others if it’s not done through them (including pro bono). Your firm’s malpractice insurance only covers work you do through your firm.