I want to resign my current job by Dec. 31st (Have a new job starting Jan. 9).
Im in an excempt position with a "at will contract". In the employee handbook the employer is requesting a 2 weeks notice. However the handbook also says that I can quit at any time for any reason and so can the employer.

If I send my resignation letter 2 weeks prior to the 31st, do I still get the holidays (24th -31st) paid ?

Would I be better of just go in on Jan. 2nd and resign (this way I get the holidays paid for sure) ?

Whether or not you would get paid for the holidays after you submit your resignation is entirely up to the employer. The law does not require that you be granted paid holidays at all; the employer gets to decide who is and is not eligible.

The only way to be certain you get them is not to resign until you have already been paid for them.