Should I take money out of my CD to pay towards my mortgage?

All else being equal, earning 4% in a CD is better then "earning" 2.5% by paying extra on the mortgage (every $100 you put towards the mortgage reduces your interest by $2.50, effectively "earning" 2.5%). But you need to take the tax and penalty into consideration.

CD interest is taxable, so if his marginal tax bracket is 29% (as you said in the comments), the effective interest return is 4% * (1-.29) = 2.84%, which is still better than 2.5%, but getting closer. If he itemizes deductions, though, then the interest savings on the mortgage is actually reduced by the tax rate as well, making the difference closer to the original 1.5%.

He's already got a 15-year mortgage that he can (presumably) afford and has $25K saved up that he could tap if needed, so there's no pressing need for cash that you've indicated. Since there's no significant interest savings, I see no compelling reason to cash in the CD. It's not a horrible idea, but it isn't going to accomplish much in the end. If some emergency arises that he needs cash form then he can consider cashing it in to cover that, but putting it towards the mortgage doesn't accomplish much.

A third option, would it still be better to re-invest the money from the CD after the 2 years is up into a similar one and never put it towards my mortgage?

It depends again on what the CD rates are at that time, and how much other savings you have (to cover emergencies, etc.) If you don't need that much in savings, you might put it toward your mortgage, or even look for more risky investments that have a higher expected return. I don't mean risky in the sense that you'll lose it all, but risky in the sense that you'll do somewhere between earning 20% and losing 10%.